Restructure tutorials

docs/Guides/Getting-Started/getting-started.md → docs/Guides/Getting-Started/index.md

@@ -1,8 +1,7 @@
 ---
-id: getting-started
 title: Getting Started
 sidebar_label: Getting Started
-slug: /
+sidebar_position: 1
 ---
 
 import Tabs from '@theme/Tabs';

docs/Tutorials/GenomeTracks/atacseq-gtracks-deeptools.md

@@ -0,0 +1,6 @@
+---
+id: atacseq-gtracks-deeptools
+title: "ATAC-seq Genome Tracks (Deeptools)"
+sidebar_label: "ATAC-seq Genome Tracks (Deeptools)"
+sidebar_position: 2
+---

docs/Tutorials/GenomeTracks/chipexo-gtracks-deeptools.md

@@ -0,0 +1,6 @@
+---
+id: chipexo-gtracks-deeptools
+title: "ChIP-exo Genome Tracks (Deeptools)"
+sidebar_label: "ChIP-exo Genome Tracks (Deeptools)"
+sidebar_position: 1
+---

docs/Guides/Tutorials/genome-tracks-tutorial.md → docs/Tutorials/GenomeTracks/custom-gtracks-scriptmanager.md

@@ -1,7 +1,8 @@
 ---
-id: genome-tracks-tutorial
-title: "Making Genome Tracks Tutorial"
-sidebar_label: "Genome Tracks (BigWig)"
+id: custom-gtracks-scriptmanager
+title: "Making Custom Genome Tracks Tutorial"
+sidebar_label: "Custom Tracks (ScriptManager/Kent Tools)"
+sidebar_position: 3
 ---
 
 import Tabs from '@theme/Tabs';
@@ -69,7 +70,7 @@ OR
 
 
 <div class="tutorial-img-flow-container">
- <img src={require('./img/download-yep-home.png').default} style={{width:60+'%'}} />
+ <img src={require('../QuickStart/img/download-yep-home.png').default} style={{width:60+'%'}} />
 </div>
 
 1. Navigate to [www.yeastepigenome.org][yep-stencil] and search for Reb1
@@ -78,8 +79,8 @@ OR
 4. Unzip the resulting file ‘12141_YEP.zip’ and inspect the contents of the new `12141_YEP` folder. It should contain a file called `12141_filtered.bam`.
 
 <div class="tutorial-img-flow-container">
- <img src={require('./img/download-yep-reb1.png').default} style={{width:50+'%'}} />
- <img src={require('./img/download-yep-reb1-metadata.png').default} style={{width:50+'%'}} />
+ <img src={require('../QuickStart/img/download-yep-reb1.png').default} style={{width:50+'%'}} />
+ <img src={require('../QuickStart/img/download-yep-reb1-metadata.png').default} style={{width:50+'%'}} />
 </div>
 
 ### XXXX.chrom.sizes Reference File

docs/Tutorials/GenomeTracks/index.md

@@ -0,0 +1,5 @@
+---
+title: "Making Genome Tracks"
+sidebar_label: "Genome Tracks"
+sidebar_position: 2
+---

docs/Tutorials/PeakCalling/atacseq-pcalling-macs.md

@@ -0,0 +1,232 @@
+---
+id: atacseq-pcalling-macs
+title: "ATAC-seq Peak Calling (MACS)"
+sidebar_label: "ATAC-seq Peak Calling (MACS)"
+sidebar_position: 3
+---
+
+import Tabs from '@theme/Tabs';
+import TabItem from '@theme/TabItem';
+import Link from '@docusaurus/Link';
+
+_Performing ATAC-seq peak calling with MACS2_ 
+
+**Goal:** This tutorial provides a guide to peak calling using MACS2 and data generated by the [Stanford Encode Project][encode-project]. 
+
+---
+
+## Background
+
+### What is MACS2?
+**MACS2 (Model-based Analysis of ChIP-Seq)** is a widely used program to detect **peaks** — enriched regions in sequencing data where reads pile up. 
+- For **ChIP-seq**, peaks correspond to transcription factor binding sites. 
+- For **ATAC-seq**, peaks correspond to **open chromatin regions** cut by the Tn5 transposase. 
+
+That’s why we use MACS2 for ATAC-seq: it helps us identify the regions of the genome that are likely regulatory hotspots.
+
+---
+## Download Data
+
+You need one set of genomic coordinate regions to investigate (BED) and one file of sequencing data alignments (BAM) to complete this exercise. [Read more about the BED/BAM file formats here.][file-formats]
+
+
+### BED File
+This is the set of transcription start site (TSS) annotations for the GRCh38 genome build that has been subsampled down to 2000 sites for quick tutorial purposes. A more formal analysis may use a more complete set of annotations (many more sites).
+
+<Link
+ className="button button--secondary"
+ target="\_blank"
+ href="/sample_data/atac-seq-tutorial/UCSC_GRCh38_knownGene_GENCODEV3_TSS_2000bp_SUBSAMPLE-2000-Sites.bed" >
+ Download sample BED file
+</Link>
+
+<br />
+<br />
+
+:::caution
+If your BED file downloads with a `.txt` extension, make sure to change the filename to a `.bed` extension. For this tutorial, the BED file is named `UCSC_GRCh38_knownGene_GENCODEV3_TSS_2000bp_SUBSAMPLE-2000-Sites.bed`.
+:::
+
+### BAM File
+This is the set of read alignments from the [ENCODE Project][encode-project] (`ENCFF205TSU.bam`). 
+
+<Link
+ className="button button--secondary"
+ href="https://www.encodeproject.org/files/ENCFF205TSU/@@download/ENCFF205TSU">
+ Download sample BAM file
+</Link>
+
+<br />
+<br />
+
+:::caution
+The BAM file is ~2.5GB large so make sure you have enough space on your machine before downloading.
+:::
+
+## Peak Calling ATAC-seq with MACS2 
+
+### 1. Install MACS2
+There are two common ways to install bioinformatics software: **pip** and **conda**.
+
+- **pip**: the Python package manager. It installs Python-based tools (like MACS2) into your environment. 
+- **conda**: an environment manager that can install packages (both Python and non-Python) with all dependencies. Widely used in bioinformatics. We’ll show both methods,
+
+#### 1.1 Install using pip 
+
+```bash
+# Create a clean Python environment 
+python3 -m venv macs2_env
+source macs2_env/bin/activate
+
+# Update pip and install MACS2
+pip install --upgrade pip wheel
+pip install numpy
+pip install MACS2
+```
+
+#### 1.2 Install using conda
+
+```bash
+conda create -n macs2_env python=3.8
+conda activate macs2_env
+conda install -c bioconda macs2
+```
+
+### 2. Generate BAI index file
+A BAI index file is required for each BAM file of interest (i.e., the tag occupancy data you want to plot). This file allows for rapid access of the sorted and aligned sequence reads (BAM file).
+
+:::tip
+
+SAM/BAM standard is to keep BAI file in same directory as BAM file with the ScriptManager-generated filename.
+
+```bash
+samtools index ENCFF205TSU.bam 
+```
+
+### 3. Run MACS2 for ATAC-seq
+ATAC-seq is slightly different from ChIP-seq because fragments are shifted by Tn5 transposase insertions and you usually call peaks with paired-end BAM.
+
+ ```bash
+ macs2 callpeak -t ENCFF205TSU.bam \
+ -f BAMPE \
+ -g hs \
+ -n sample_ATAC \
+ --outdir macs2_output \
+ --shift -100 --extsize 200 \
+ -q 0.01
+ ```
+
+ Key flags explained:
+ - -f BAMPE: Paired-end BAM input
+ - -g hs: Human genome
+ - --shift -100 --extsize 200: Adjusts for Tn5 integration offset
+ - -q 0.01: False Discovery Rate Threshold
+
+ The output files should be the follwoing: 
+ - **sample_ATAC_peaks.narrowPeak**: Peak regions (main file to use downstream) 
+ - **sample_ATAC_peaks.xls**: Detailed peak statistics
+ - **sample_ATAC_summits.bed**: Summit positions
+
+ ### 4. Convert 'sample_ATAC_peaks.narrowPeak' file to BED File
+
+```bash
+ cd macs2_output
+ cut -f1-3 sample_ATAC_peaks.narrowPeak > sample_ATAC_peaks.bed
+ awk '{print $1"\t"$2-1000"\t"$2+1000}' sample_ATAC_top1000_summits.bed > summits_1000bp.bed
+```
+
+ :::note
+ The file of this BED file is very large, so we use 1000bp to around each summit in order reduce processing time. 
+ :::
+
+ The output file should be the follwoing: 
+ - **sample_ATAC_peaks.bed**
+
+ ### 5. ScriptManager for TagPileup
+ScriptManager can plot composite pileups and heatmaps using BAM + BED.
+
+ ##### 5.1 Index Bam File: BAM Manipulation ➡️ [__BAM-BAI Indexer__][bam-indexer]
+```bash
+ ENCFF205TSU.bam
+ ENCFF205TSU.bam.bai # Need to generate this file to proceed.
+```
+:::
+
+<div class="tutorial-img-flow-container">
+ <img src={require('./img/bam_atacseq_peakcalling.png').default} style={{width:60+'%',}}/>
+ <i class="fa-solid fa-arrow-right fa-lg"></i>
+ <img src={require('./img/gui-bamidx-complete.png').default} style={{width:30+'%',}}/>
+</div>
+
+:::note
+The speed of this step scales with the size of the BAM file. Generally this step 30 sec for a 100 MB BAM file but may take 1-2 min for a multi-GB BAM file.
+:::
+
+
+ #### 5.2 TagPileup: Sequence Read Analysis ➡️ [__Tag Pileup__][tag-pileup]
+Use **"Full Fragment"** in the top right, then select **"Combined"** color , **"Output Composite"**, **"CDT"**, and **"Output GZIP"**. Then, proceed to "Output Directory".
+
+<div class="tutorial-img-flow-container">
+ <img src={require('./img/atacseq_peak_tagpileup.png').default} style={{width:100+'%',}}/>
+</div>
+
+<div class="tutorial-img-flow-container">
+ <img src={require('./img/atacseq_peak_pileup.png').default} style={{width:100+'%',}}/>
+</div>
+
+
+ ### 6. ScriptManager for Heatmap
+
+ #### 6.1 Sort BED file by CDT file: Coordinate File Manipulation ➡️ [__Sort BED__][sort-bed]
+
+<div class="tutorial-img-flow-container">
+ <img src={require('./img/atacseq_peak_sortcdt.png').default} style={{width:100+'%',}}/>
+</div>
+
+
+#### 6.2 Heatmap: Figure Generation ➡️ [__Heat Map__][heatmap] and Figure Generation ➡️ [__Label Heatmaps__][label-heatmap]
+
+<div class="tutorial-img-flow-container">
+ <img src={require('./img/atacseq_pea_heatmapgen.png').default} style={{width:55+'%',}}/>
+ <i class="fa-solid fa-arrow-right fa-lg"></i>
+ <img src={require('./img/atacseq_peak_heatmap.png').default} style={{width:45+'%',}}/>
+</div>
+
+## Command-Line shell script for ScriptManager
+
+The following shell commands records the locations for a BED file, a BAM file, and the anticipated OUTPUT basename as environmental variables to derive the corresponding composite plot values and heatmaps. This can serve as a template for you to write out your own workflows as bash scripts that execute command-line style ScriptManager.
+
+```bash
+SCRIPTMANAGER=/path/to/ScriptManager.jar
+BEDFILE=/path/to/sample_ATAC_top1000_summits.bed
+BAMFILE=/path/to/ENCFF205TSU.bam
+OUTPUT=/path/to/myoutput
+
+samtools index $BAMFILE
+
+java -jar $SCRIPTMANAGER read-analysis tag-pileup --combined --full-fragment $OUTPUT\_1000bp.bed $BAMFILE -o $OUTPUT\_composite.out -M $OUTPUT\_matrix
+java -jar $SCRIPTMANAGER coordinate-manipulation sort-bed -c 1000 $OUTPUT\_1000bp.bed $OUTPUT\_matrix_combined.cdt -o $OUTPUT\_SORT
+java -jar $SCRIPTMANAGER figure-generation heatmap -p .95 --black $OUTPUT\_SORT.cdt -o $OUTPUT\_heatmap.png
+
+# Output files:
+# - /path/to/myoutput_composite.out
+# - /path/to/myoutput_matrix_combined.cdt
+# - /path/to/myoutput_SORT.bed
+# - /path/to/myoutput_SORT.cdt
+# - /path/to/myoutput_heatmap.png
+```
+
+[encode-project]: https://www.encodeproject.org/experiments/ENCFF205TSU
+
+
+
+
+
+
+
+
+
+
+
+
+

docs/Tutorials/PeakCalling/chipexo-pcalling-chexmix.md

@@ -0,0 +1,6 @@
+---
+id: chipexo-pcalling-chexmix
+title: "ChIP-exo Peak Calling (ChExMix)"
+sidebar_label: "ChIP-exo Peak Calling (ChExMix)"
+sidebar_position: 2
+---

docs/Tutorials/PeakCalling/chipexo-pcalling-genetrack.md

@@ -0,0 +1,6 @@
+---
+id: chipexo-pcalling-genetrack
+title: "ChIP-exo Peak Calling (Genetrack/CWPair)"
+sidebar_label: "ChIP-exo Peak Calling (Genetrack/CWPair)"
+sidebar_position: 1
+---

docs/Tutorials/PeakCalling/index.md

@@ -0,0 +1,5 @@
+---
+title: "Peak Calling"
+sidebar_label: "Peak Calling"
+sidebar_position: 3
+---

docs/Tutorials/PeakCalling/procap-pcalling-genetrack.md

@@ -0,0 +1 @@
+a

docs/Guides/Getting-Started/getting-started.md → docs/Guides/Getting-Started/index.md

@@ -1,8 +1,7 @@
 ---
-id: getting-started
 title: Getting Started
 sidebar_label: Getting Started
-slug: /
+sidebar_position: 1
 ---
 
 import Tabs from '@theme/Tabs';

docs/Tutorials/GenomeTracks/atacseq-gtracks-deeptools.md

@@ -0,0 +1,6 @@
+---
+id: atacseq-gtracks-deeptools
+title: "ATAC-seq Genome Tracks (Deeptools)"
+sidebar_label: "ATAC-seq Genome Tracks (Deeptools)"
+sidebar_position: 2
+---

docs/Tutorials/GenomeTracks/chipexo-gtracks-deeptools.md

@@ -0,0 +1,6 @@
+---
+id: chipexo-gtracks-deeptools
+title: "ChIP-exo Genome Tracks (Deeptools)"
+sidebar_label: "ChIP-exo Genome Tracks (Deeptools)"
+sidebar_position: 1
+---

docs/Guides/Tutorials/genome-tracks-tutorial.md → docs/Tutorials/GenomeTracks/custom-gtracks-scriptmanager.md

@@ -1,7 +1,8 @@
 ---
-id: genome-tracks-tutorial
-title: "Making Genome Tracks Tutorial"
-sidebar_label: "Genome Tracks (BigWig)"
+id: custom-gtracks-scriptmanager
+title: "Making Custom Genome Tracks Tutorial"
+sidebar_label: "Custom Tracks (ScriptManager/Kent Tools)"
+sidebar_position: 3
 ---
 
 import Tabs from '@theme/Tabs';
@@ -69,7 +70,7 @@ OR
 
 
 <div class="tutorial-img-flow-container">
- <img src={require('./img/download-yep-home.png').default} style={{width:60+'%'}} />
+ <img src={require('../QuickStart/img/download-yep-home.png').default} style={{width:60+'%'}} />
 </div>
 
 1. Navigate to [www.yeastepigenome.org][yep-stencil] and search for Reb1
@@ -78,8 +79,8 @@ OR
 4. Unzip the resulting file ‘12141_YEP.zip’ and inspect the contents of the new `12141_YEP` folder. It should contain a file called `12141_filtered.bam`.
 
 <div class="tutorial-img-flow-container">
- <img src={require('./img/download-yep-reb1.png').default} style={{width:50+'%'}} />
- <img src={require('./img/download-yep-reb1-metadata.png').default} style={{width:50+'%'}} />
+ <img src={require('../QuickStart/img/download-yep-reb1.png').default} style={{width:50+'%'}} />
+ <img src={require('../QuickStart/img/download-yep-reb1-metadata.png').default} style={{width:50+'%'}} />
 </div>
 
 ### XXXX.chrom.sizes Reference File

docs/Tutorials/GenomeTracks/index.md

@@ -0,0 +1,5 @@
+---
+title: "Making Genome Tracks"
+sidebar_label: "Genome Tracks"
+sidebar_position: 2
+---

docs/Tutorials/PeakCalling/atacseq-pcalling-macs.md

@@ -0,0 +1,232 @@
+---
+id: atacseq-pcalling-macs
+title: "ATAC-seq Peak Calling (MACS)"
+sidebar_label: "ATAC-seq Peak Calling (MACS)"
+sidebar_position: 3
+---
+
+import Tabs from '@theme/Tabs';
+import TabItem from '@theme/TabItem';
+import Link from '@docusaurus/Link';
+
+_Performing ATAC-seq peak calling with MACS2_ 
+
+**Goal:** This tutorial provides a guide to peak calling using MACS2 and data generated by the [Stanford Encode Project][encode-project]. 
+
+---
+
+## Background
+
+### What is MACS2?
+**MACS2 (Model-based Analysis of ChIP-Seq)** is a widely used program to detect **peaks** — enriched regions in sequencing data where reads pile up. 
+- For **ChIP-seq**, peaks correspond to transcription factor binding sites. 
+- For **ATAC-seq**, peaks correspond to **open chromatin regions** cut by the Tn5 transposase. 
+
+That’s why we use MACS2 for ATAC-seq: it helps us identify the regions of the genome that are likely regulatory hotspots.
+
+---
+## Download Data
+
+You need one set of genomic coordinate regions to investigate (BED) and one file of sequencing data alignments (BAM) to complete this exercise. [Read more about the BED/BAM file formats here.][file-formats]
+
+
+### BED File
+This is the set of transcription start site (TSS) annotations for the GRCh38 genome build that has been subsampled down to 2000 sites for quick tutorial purposes. A more formal analysis may use a more complete set of annotations (many more sites).
+
+<Link
+ className="button button--secondary"
+ target="\_blank"
+ href="/sample_data/atac-seq-tutorial/UCSC_GRCh38_knownGene_GENCODEV3_TSS_2000bp_SUBSAMPLE-2000-Sites.bed" >
+ Download sample BED file
+</Link>
+
+<br />
+<br />
+
+:::caution
+If your BED file downloads with a `.txt` extension, make sure to change the filename to a `.bed` extension. For this tutorial, the BED file is named `UCSC_GRCh38_knownGene_GENCODEV3_TSS_2000bp_SUBSAMPLE-2000-Sites.bed`.
+:::
+
+### BAM File
+This is the set of read alignments from the [ENCODE Project][encode-project] (`ENCFF205TSU.bam`). 
+
+<Link
+ className="button button--secondary"
+ href="https://www.encodeproject.org/files/ENCFF205TSU/@@download/ENCFF205TSU">
+ Download sample BAM file
+</Link>
+
+<br />
+<br />
+
+:::caution
+The BAM file is ~2.5GB large so make sure you have enough space on your machine before downloading.
+:::
+
+## Peak Calling ATAC-seq with MACS2 
+
+### 1. Install MACS2
+There are two common ways to install bioinformatics software: **pip** and **conda**.
+
+- **pip**: the Python package manager. It installs Python-based tools (like MACS2) into your environment. 
+- **conda**: an environment manager that can install packages (both Python and non-Python) with all dependencies. Widely used in bioinformatics. We’ll show both methods,
+
+#### 1.1 Install using pip 
+
+```bash
+# Create a clean Python environment 
+python3 -m venv macs2_env
+source macs2_env/bin/activate
+
+# Update pip and install MACS2
+pip install --upgrade pip wheel
+pip install numpy
+pip install MACS2
+```
+
+#### 1.2 Install using conda
+
+```bash
+conda create -n macs2_env python=3.8
+conda activate macs2_env
+conda install -c bioconda macs2
+```
+
+### 2. Generate BAI index file
+A BAI index file is required for each BAM file of interest (i.e., the tag occupancy data you want to plot). This file allows for rapid access of the sorted and aligned sequence reads (BAM file).
+
+:::tip
+
+SAM/BAM standard is to keep BAI file in same directory as BAM file with the ScriptManager-generated filename.
+
+```bash
+samtools index ENCFF205TSU.bam 
+```
+
+### 3. Run MACS2 for ATAC-seq
+ATAC-seq is slightly different from ChIP-seq because fragments are shifted by Tn5 transposase insertions and you usually call peaks with paired-end BAM.
+
+ ```bash
+ macs2 callpeak -t ENCFF205TSU.bam \
+ -f BAMPE \
+ -g hs \
+ -n sample_ATAC \
+ --outdir macs2_output \
+ --shift -100 --extsize 200 \
+ -q 0.01
+ ```
+
+ Key flags explained:
+ - -f BAMPE: Paired-end BAM input
+ - -g hs: Human genome
+ - --shift -100 --extsize 200: Adjusts for Tn5 integration offset
+ - -q 0.01: False Discovery Rate Threshold
+
+ The output files should be the follwoing: 
+ - **sample_ATAC_peaks.narrowPeak**: Peak regions (main file to use downstream) 
+ - **sample_ATAC_peaks.xls**: Detailed peak statistics
+ - **sample_ATAC_summits.bed**: Summit positions
+
+ ### 4. Convert 'sample_ATAC_peaks.narrowPeak' file to BED File
+
+```bash
+ cd macs2_output
+ cut -f1-3 sample_ATAC_peaks.narrowPeak > sample_ATAC_peaks.bed
+ awk '{print $1"\t"$2-1000"\t"$2+1000}' sample_ATAC_top1000_summits.bed > summits_1000bp.bed
+```
+
+ :::note
+ The file of this BED file is very large, so we use 1000bp to around each summit in order reduce processing time. 
+ :::
+
+ The output file should be the follwoing: 
+ - **sample_ATAC_peaks.bed**
+
+ ### 5. ScriptManager for TagPileup
+ScriptManager can plot composite pileups and heatmaps using BAM + BED.
+
+ ##### 5.1 Index Bam File: BAM Manipulation ➡️ [__BAM-BAI Indexer__][bam-indexer]
+```bash
+ ENCFF205TSU.bam
+ ENCFF205TSU.bam.bai # Need to generate this file to proceed.
+```
+:::
+
+<div class="tutorial-img-flow-container">
+ <img src={require('./img/bam_atacseq_peakcalling.png').default} style={{width:60+'%',}}/>
+ <i class="fa-solid fa-arrow-right fa-lg"></i>
+ <img src={require('./img/gui-bamidx-complete.png').default} style={{width:30+'%',}}/>
+</div>
+
+:::note
+The speed of this step scales with the size of the BAM file. Generally this step 30 sec for a 100 MB BAM file but may take 1-2 min for a multi-GB BAM file.
+:::
+
+
+ #### 5.2 TagPileup: Sequence Read Analysis ➡️ [__Tag Pileup__][tag-pileup]
+Use **"Full Fragment"** in the top right, then select **"Combined"** color , **"Output Composite"**, **"CDT"**, and **"Output GZIP"**. Then, proceed to "Output Directory".
+
+<div class="tutorial-img-flow-container">
+ <img src={require('./img/atacseq_peak_tagpileup.png').default} style={{width:100+'%',}}/>
+</div>
+
+<div class="tutorial-img-flow-container">
+ <img src={require('./img/atacseq_peak_pileup.png').default} style={{width:100+'%',}}/>
+</div>
+
+
+ ### 6. ScriptManager for Heatmap
+
+ #### 6.1 Sort BED file by CDT file: Coordinate File Manipulation ➡️ [__Sort BED__][sort-bed]
+
+<div class="tutorial-img-flow-container">
+ <img src={require('./img/atacseq_peak_sortcdt.png').default} style={{width:100+'%',}}/>
+</div>
+
+
+#### 6.2 Heatmap: Figure Generation ➡️ [__Heat Map__][heatmap] and Figure Generation ➡️ [__Label Heatmaps__][label-heatmap]
+
+<div class="tutorial-img-flow-container">
+ <img src={require('./img/atacseq_pea_heatmapgen.png').default} style={{width:55+'%',}}/>
+ <i class="fa-solid fa-arrow-right fa-lg"></i>
+ <img src={require('./img/atacseq_peak_heatmap.png').default} style={{width:45+'%',}}/>
+</div>
+
+## Command-Line shell script for ScriptManager
+
+The following shell commands records the locations for a BED file, a BAM file, and the anticipated OUTPUT basename as environmental variables to derive the corresponding composite plot values and heatmaps. This can serve as a template for you to write out your own workflows as bash scripts that execute command-line style ScriptManager.
+
+```bash
+SCRIPTMANAGER=/path/to/ScriptManager.jar
+BEDFILE=/path/to/sample_ATAC_top1000_summits.bed
+BAMFILE=/path/to/ENCFF205TSU.bam
+OUTPUT=/path/to/myoutput
+
+samtools index $BAMFILE
+
+java -jar $SCRIPTMANAGER read-analysis tag-pileup --combined --full-fragment $OUTPUT\_1000bp.bed $BAMFILE -o $OUTPUT\_composite.out -M $OUTPUT\_matrix
+java -jar $SCRIPTMANAGER coordinate-manipulation sort-bed -c 1000 $OUTPUT\_1000bp.bed $OUTPUT\_matrix_combined.cdt -o $OUTPUT\_SORT
+java -jar $SCRIPTMANAGER figure-generation heatmap -p .95 --black $OUTPUT\_SORT.cdt -o $OUTPUT\_heatmap.png
+
+# Output files:
+# - /path/to/myoutput_composite.out
+# - /path/to/myoutput_matrix_combined.cdt
+# - /path/to/myoutput_SORT.bed
+# - /path/to/myoutput_SORT.cdt
+# - /path/to/myoutput_heatmap.png
+```
+
+[encode-project]: https://www.encodeproject.org/experiments/ENCFF205TSU
+
+
+
+
+
+
+
+
+
+
+
+
+

docs/Tutorials/PeakCalling/chipexo-pcalling-chexmix.md

@@ -0,0 +1,6 @@
+---
+id: chipexo-pcalling-chexmix
+title: "ChIP-exo Peak Calling (ChExMix)"
+sidebar_label: "ChIP-exo Peak Calling (ChExMix)"
+sidebar_position: 2
+---

docs/Tutorials/PeakCalling/chipexo-pcalling-genetrack.md

@@ -0,0 +1,6 @@
+---
+id: chipexo-pcalling-genetrack
+title: "ChIP-exo Peak Calling (Genetrack/CWPair)"
+sidebar_label: "ChIP-exo Peak Calling (Genetrack/CWPair)"
+sidebar_position: 1
+---

docs/Tutorials/PeakCalling/index.md

@@ -0,0 +1,5 @@
+---
+title: "Peak Calling"
+sidebar_label: "Peak Calling"
+sidebar_position: 3
+---

docs/Tutorials/PeakCalling/procap-pcalling-genetrack.md

@@ -0,0 +1 @@
+a

docs/Guides/Getting-Started/getting-started.md → docs/Guides/Getting-Started/index.md

@@ -1,8 +1,7 @@
 ---
-id: getting-started
 title: Getting Started
 sidebar_label: Getting Started
-slug: /
+sidebar_position: 1
 ---
 
 import Tabs from '@theme/Tabs';

docs/Tutorials/GenomeTracks/atacseq-gtracks-deeptools.md

@@ -0,0 +1,6 @@
+---
+id: atacseq-gtracks-deeptools
+title: "ATAC-seq Genome Tracks (Deeptools)"
+sidebar_label: "ATAC-seq Genome Tracks (Deeptools)"
+sidebar_position: 2
+---

docs/Tutorials/GenomeTracks/chipexo-gtracks-deeptools.md

@@ -0,0 +1,6 @@
+---
+id: chipexo-gtracks-deeptools
+title: "ChIP-exo Genome Tracks (Deeptools)"
+sidebar_label: "ChIP-exo Genome Tracks (Deeptools)"
+sidebar_position: 1
+---

docs/Guides/Tutorials/genome-tracks-tutorial.md → docs/Tutorials/GenomeTracks/custom-gtracks-scriptmanager.md

@@ -1,7 +1,8 @@
 ---
-id: genome-tracks-tutorial
-title: "Making Genome Tracks Tutorial"
-sidebar_label: "Genome Tracks (BigWig)"
+id: custom-gtracks-scriptmanager
+title: "Making Custom Genome Tracks Tutorial"
+sidebar_label: "Custom Tracks (ScriptManager/Kent Tools)"
+sidebar_position: 3
 ---
 
 import Tabs from '@theme/Tabs';
@@ -69,7 +70,7 @@ OR
 
 
 <div class="tutorial-img-flow-container">
- <img src={require('./img/download-yep-home.png').default} style={{width:60+'%'}} />
+ <img src={require('../QuickStart/img/download-yep-home.png').default} style={{width:60+'%'}} />
 </div>
 
 1. Navigate to [www.yeastepigenome.org][yep-stencil] and search for Reb1
@@ -78,8 +79,8 @@ OR
 4. Unzip the resulting file ‘12141_YEP.zip’ and inspect the contents of the new `12141_YEP` folder. It should contain a file called `12141_filtered.bam`.
 
 <div class="tutorial-img-flow-container">
- <img src={require('./img/download-yep-reb1.png').default} style={{width:50+'%'}} />
- <img src={require('./img/download-yep-reb1-metadata.png').default} style={{width:50+'%'}} />
+ <img src={require('../QuickStart/img/download-yep-reb1.png').default} style={{width:50+'%'}} />
+ <img src={require('../QuickStart/img/download-yep-reb1-metadata.png').default} style={{width:50+'%'}} />
 </div>
 
 ### XXXX.chrom.sizes Reference File

docs/Tutorials/GenomeTracks/index.md

@@ -0,0 +1,5 @@
+---
+title: "Making Genome Tracks"
+sidebar_label: "Genome Tracks"
+sidebar_position: 2
+---

docs/Tutorials/PeakCalling/atacseq-pcalling-macs.md

@@ -0,0 +1,232 @@
+---
+id: atacseq-pcalling-macs
+title: "ATAC-seq Peak Calling (MACS)"
+sidebar_label: "ATAC-seq Peak Calling (MACS)"
+sidebar_position: 3
+---
+
+import Tabs from '@theme/Tabs';
+import TabItem from '@theme/TabItem';
+import Link from '@docusaurus/Link';
+
+_Performing ATAC-seq peak calling with MACS2_ 
+
+**Goal:** This tutorial provides a guide to peak calling using MACS2 and data generated by the [Stanford Encode Project][encode-project]. 
+
+---
+
+## Background
+
+### What is MACS2?
+**MACS2 (Model-based Analysis of ChIP-Seq)** is a widely used program to detect **peaks** — enriched regions in sequencing data where reads pile up. 
+- For **ChIP-seq**, peaks correspond to transcription factor binding sites. 
+- For **ATAC-seq**, peaks correspond to **open chromatin regions** cut by the Tn5 transposase. 
+
+That’s why we use MACS2 for ATAC-seq: it helps us identify the regions of the genome that are likely regulatory hotspots.
+
+---
+## Download Data
+
+You need one set of genomic coordinate regions to investigate (BED) and one file of sequencing data alignments (BAM) to complete this exercise. [Read more about the BED/BAM file formats here.][file-formats]
+
+
+### BED File
+This is the set of transcription start site (TSS) annotations for the GRCh38 genome build that has been subsampled down to 2000 sites for quick tutorial purposes. A more formal analysis may use a more complete set of annotations (many more sites).
+
+<Link
+ className="button button--secondary"
+ target="\_blank"
+ href="/sample_data/atac-seq-tutorial/UCSC_GRCh38_knownGene_GENCODEV3_TSS_2000bp_SUBSAMPLE-2000-Sites.bed" >
+ Download sample BED file
+</Link>
+
+<br />
+<br />
+
+:::caution
+If your BED file downloads with a `.txt` extension, make sure to change the filename to a `.bed` extension. For this tutorial, the BED file is named `UCSC_GRCh38_knownGene_GENCODEV3_TSS_2000bp_SUBSAMPLE-2000-Sites.bed`.
+:::
+
+### BAM File
+This is the set of read alignments from the [ENCODE Project][encode-project] (`ENCFF205TSU.bam`). 
+
+<Link
+ className="button button--secondary"
+ href="https://www.encodeproject.org/files/ENCFF205TSU/@@download/ENCFF205TSU">
+ Download sample BAM file
+</Link>
+
+<br />
+<br />
+
+:::caution
+The BAM file is ~2.5GB large so make sure you have enough space on your machine before downloading.
+:::
+
+## Peak Calling ATAC-seq with MACS2 
+
+### 1. Install MACS2
+There are two common ways to install bioinformatics software: **pip** and **conda**.
+
+- **pip**: the Python package manager. It installs Python-based tools (like MACS2) into your environment. 
+- **conda**: an environment manager that can install packages (both Python and non-Python) with all dependencies. Widely used in bioinformatics. We’ll show both methods,
+
+#### 1.1 Install using pip 
+
+```bash
+# Create a clean Python environment 
+python3 -m venv macs2_env
+source macs2_env/bin/activate
+
+# Update pip and install MACS2
+pip install --upgrade pip wheel
+pip install numpy
+pip install MACS2
+```
+
+#### 1.2 Install using conda
+
+```bash
+conda create -n macs2_env python=3.8
+conda activate macs2_env
+conda install -c bioconda macs2
+```
+
+### 2. Generate BAI index file
+A BAI index file is required for each BAM file of interest (i.e., the tag occupancy data you want to plot). This file allows for rapid access of the sorted and aligned sequence reads (BAM file).
+
+:::tip
+
+SAM/BAM standard is to keep BAI file in same directory as BAM file with the ScriptManager-generated filename.
+
+```bash
+samtools index ENCFF205TSU.bam 
+```
+
+### 3. Run MACS2 for ATAC-seq
+ATAC-seq is slightly different from ChIP-seq because fragments are shifted by Tn5 transposase insertions and you usually call peaks with paired-end BAM.
+
+ ```bash
+ macs2 callpeak -t ENCFF205TSU.bam \
+ -f BAMPE \
+ -g hs \
+ -n sample_ATAC \
+ --outdir macs2_output \
+ --shift -100 --extsize 200 \
+ -q 0.01
+ ```
+
+ Key flags explained:
+ - -f BAMPE: Paired-end BAM input
+ - -g hs: Human genome
+ - --shift -100 --extsize 200: Adjusts for Tn5 integration offset
+ - -q 0.01: False Discovery Rate Threshold
+
+ The output files should be the follwoing: 
+ - **sample_ATAC_peaks.narrowPeak**: Peak regions (main file to use downstream) 
+ - **sample_ATAC_peaks.xls**: Detailed peak statistics
+ - **sample_ATAC_summits.bed**: Summit positions
+
+ ### 4. Convert 'sample_ATAC_peaks.narrowPeak' file to BED File
+
+```bash
+ cd macs2_output
+ cut -f1-3 sample_ATAC_peaks.narrowPeak > sample_ATAC_peaks.bed
+ awk '{print $1"\t"$2-1000"\t"$2+1000}' sample_ATAC_top1000_summits.bed > summits_1000bp.bed
+```
+
+ :::note
+ The file of this BED file is very large, so we use 1000bp to around each summit in order reduce processing time. 
+ :::
+
+ The output file should be the follwoing: 
+ - **sample_ATAC_peaks.bed**
+
+ ### 5. ScriptManager for TagPileup
+ScriptManager can plot composite pileups and heatmaps using BAM + BED.
+
+ ##### 5.1 Index Bam File: BAM Manipulation ➡️ [__BAM-BAI Indexer__][bam-indexer]
+```bash
+ ENCFF205TSU.bam
+ ENCFF205TSU.bam.bai # Need to generate this file to proceed.
+```
+:::
+
+<div class="tutorial-img-flow-container">
+ <img src={require('./img/bam_atacseq_peakcalling.png').default} style={{width:60+'%',}}/>
+ <i class="fa-solid fa-arrow-right fa-lg"></i>
+ <img src={require('./img/gui-bamidx-complete.png').default} style={{width:30+'%',}}/>
+</div>
+
+:::note
+The speed of this step scales with the size of the BAM file. Generally this step 30 sec for a 100 MB BAM file but may take 1-2 min for a multi-GB BAM file.
+:::
+
+
+ #### 5.2 TagPileup: Sequence Read Analysis ➡️ [__Tag Pileup__][tag-pileup]
+Use **"Full Fragment"** in the top right, then select **"Combined"** color , **"Output Composite"**, **"CDT"**, and **"Output GZIP"**. Then, proceed to "Output Directory".
+
+<div class="tutorial-img-flow-container">
+ <img src={require('./img/atacseq_peak_tagpileup.png').default} style={{width:100+'%',}}/>
+</div>
+
+<div class="tutorial-img-flow-container">
+ <img src={require('./img/atacseq_peak_pileup.png').default} style={{width:100+'%',}}/>
+</div>
+
+
+ ### 6. ScriptManager for Heatmap
+
+ #### 6.1 Sort BED file by CDT file: Coordinate File Manipulation ➡️ [__Sort BED__][sort-bed]
+
+<div class="tutorial-img-flow-container">
+ <img src={require('./img/atacseq_peak_sortcdt.png').default} style={{width:100+'%',}}/>
+</div>
+
+
+#### 6.2 Heatmap: Figure Generation ➡️ [__Heat Map__][heatmap] and Figure Generation ➡️ [__Label Heatmaps__][label-heatmap]
+
+<div class="tutorial-img-flow-container">
+ <img src={require('./img/atacseq_pea_heatmapgen.png').default} style={{width:55+'%',}}/>
+ <i class="fa-solid fa-arrow-right fa-lg"></i>
+ <img src={require('./img/atacseq_peak_heatmap.png').default} style={{width:45+'%',}}/>
+</div>
+
+## Command-Line shell script for ScriptManager
+
+The following shell commands records the locations for a BED file, a BAM file, and the anticipated OUTPUT basename as environmental variables to derive the corresponding composite plot values and heatmaps. This can serve as a template for you to write out your own workflows as bash scripts that execute command-line style ScriptManager.
+
+```bash
+SCRIPTMANAGER=/path/to/ScriptManager.jar
+BEDFILE=/path/to/sample_ATAC_top1000_summits.bed
+BAMFILE=/path/to/ENCFF205TSU.bam
+OUTPUT=/path/to/myoutput
+
+samtools index $BAMFILE
+
+java -jar $SCRIPTMANAGER read-analysis tag-pileup --combined --full-fragment $OUTPUT\_1000bp.bed $BAMFILE -o $OUTPUT\_composite.out -M $OUTPUT\_matrix
+java -jar $SCRIPTMANAGER coordinate-manipulation sort-bed -c 1000 $OUTPUT\_1000bp.bed $OUTPUT\_matrix_combined.cdt -o $OUTPUT\_SORT
+java -jar $SCRIPTMANAGER figure-generation heatmap -p .95 --black $OUTPUT\_SORT.cdt -o $OUTPUT\_heatmap.png
+
+# Output files:
+# - /path/to/myoutput_composite.out
+# - /path/to/myoutput_matrix_combined.cdt
+# - /path/to/myoutput_SORT.bed
+# - /path/to/myoutput_SORT.cdt
+# - /path/to/myoutput_heatmap.png
+```
+
+[encode-project]: https://www.encodeproject.org/experiments/ENCFF205TSU
+
+
+
+
+
+
+
+
+
+
+
+
+

docs/Tutorials/PeakCalling/chipexo-pcalling-chexmix.md

@@ -0,0 +1,6 @@
+---
+id: chipexo-pcalling-chexmix
+title: "ChIP-exo Peak Calling (ChExMix)"
+sidebar_label: "ChIP-exo Peak Calling (ChExMix)"
+sidebar_position: 2
+---

docs/Tutorials/PeakCalling/chipexo-pcalling-genetrack.md

@@ -0,0 +1,6 @@
+---
+id: chipexo-pcalling-genetrack
+title: "ChIP-exo Peak Calling (Genetrack/CWPair)"
+sidebar_label: "ChIP-exo Peak Calling (Genetrack/CWPair)"
+sidebar_position: 1
+---

docs/Tutorials/PeakCalling/index.md

@@ -0,0 +1,5 @@
+---
+title: "Peak Calling"
+sidebar_label: "Peak Calling"
+sidebar_position: 3
+---

docs/Tutorials/PeakCalling/procap-pcalling-genetrack.md

@@ -0,0 +1 @@
+a

docs/Guides/Getting-Started/getting-started.md → docs/Guides/Getting-Started/index.md

@@ -1,8 +1,7 @@
 ---
-id: getting-started
 title: Getting Started
 sidebar_label: Getting Started
-slug: /
+sidebar_position: 1
 ---
 
 import Tabs from '@theme/Tabs';

docs/Tutorials/GenomeTracks/atacseq-gtracks-deeptools.md

@@ -0,0 +1,6 @@
+---
+id: atacseq-gtracks-deeptools
+title: "ATAC-seq Genome Tracks (Deeptools)"
+sidebar_label: "ATAC-seq Genome Tracks (Deeptools)"
+sidebar_position: 2
+---

docs/Tutorials/GenomeTracks/chipexo-gtracks-deeptools.md

@@ -0,0 +1,6 @@
+---
+id: chipexo-gtracks-deeptools
+title: "ChIP-exo Genome Tracks (Deeptools)"
+sidebar_label: "ChIP-exo Genome Tracks (Deeptools)"
+sidebar_position: 1
+---

docs/Guides/Tutorials/genome-tracks-tutorial.md → docs/Tutorials/GenomeTracks/custom-gtracks-scriptmanager.md

@@ -1,7 +1,8 @@
 ---
-id: genome-tracks-tutorial
-title: "Making Genome Tracks Tutorial"
-sidebar_label: "Genome Tracks (BigWig)"
+id: custom-gtracks-scriptmanager
+title: "Making Custom Genome Tracks Tutorial"
+sidebar_label: "Custom Tracks (ScriptManager/Kent Tools)"
+sidebar_position: 3
 ---
 
 import Tabs from '@theme/Tabs';
@@ -69,7 +70,7 @@ OR
 
 
 <div class="tutorial-img-flow-container">
- <img src={require('./img/download-yep-home.png').default} style={{width:60+'%'}} />
+ <img src={require('../QuickStart/img/download-yep-home.png').default} style={{width:60+'%'}} />
 </div>
 
 1. Navigate to [www.yeastepigenome.org][yep-stencil] and search for Reb1
@@ -78,8 +79,8 @@ OR
 4. Unzip the resulting file ‘12141_YEP.zip’ and inspect the contents of the new `12141_YEP` folder. It should contain a file called `12141_filtered.bam`.
 
 <div class="tutorial-img-flow-container">
- <img src={require('./img/download-yep-reb1.png').default} style={{width:50+'%'}} />
- <img src={require('./img/download-yep-reb1-metadata.png').default} style={{width:50+'%'}} />
+ <img src={require('../QuickStart/img/download-yep-reb1.png').default} style={{width:50+'%'}} />
+ <img src={require('../QuickStart/img/download-yep-reb1-metadata.png').default} style={{width:50+'%'}} />
 </div>
 
 ### XXXX.chrom.sizes Reference File

docs/Tutorials/GenomeTracks/index.md

@@ -0,0 +1,5 @@
+---
+title: "Making Genome Tracks"
+sidebar_label: "Genome Tracks"
+sidebar_position: 2
+---

docs/Tutorials/PeakCalling/atacseq-pcalling-macs.md

@@ -0,0 +1,232 @@
+---
+id: atacseq-pcalling-macs
+title: "ATAC-seq Peak Calling (MACS)"
+sidebar_label: "ATAC-seq Peak Calling (MACS)"
+sidebar_position: 3
+---
+
+import Tabs from '@theme/Tabs';
+import TabItem from '@theme/TabItem';
+import Link from '@docusaurus/Link';
+
+_Performing ATAC-seq peak calling with MACS2_ 
+
+**Goal:** This tutorial provides a guide to peak calling using MACS2 and data generated by the [Stanford Encode Project][encode-project]. 
+
+---
+
+## Background
+
+### What is MACS2?
+**MACS2 (Model-based Analysis of ChIP-Seq)** is a widely used program to detect **peaks** — enriched regions in sequencing data where reads pile up. 
+- For **ChIP-seq**, peaks correspond to transcription factor binding sites. 
+- For **ATAC-seq**, peaks correspond to **open chromatin regions** cut by the Tn5 transposase. 
+
+That’s why we use MACS2 for ATAC-seq: it helps us identify the regions of the genome that are likely regulatory hotspots.
+
+---
+## Download Data
+
+You need one set of genomic coordinate regions to investigate (BED) and one file of sequencing data alignments (BAM) to complete this exercise. [Read more about the BED/BAM file formats here.][file-formats]
+
+
+### BED File
+This is the set of transcription start site (TSS) annotations for the GRCh38 genome build that has been subsampled down to 2000 sites for quick tutorial purposes. A more formal analysis may use a more complete set of annotations (many more sites).
+
+<Link
+ className="button button--secondary"
+ target="\_blank"
+ href="/sample_data/atac-seq-tutorial/UCSC_GRCh38_knownGene_GENCODEV3_TSS_2000bp_SUBSAMPLE-2000-Sites.bed" >
+ Download sample BED file
+</Link>
+
+<br />
+<br />
+
+:::caution
+If your BED file downloads with a `.txt` extension, make sure to change the filename to a `.bed` extension. For this tutorial, the BED file is named `UCSC_GRCh38_knownGene_GENCODEV3_TSS_2000bp_SUBSAMPLE-2000-Sites.bed`.
+:::
+
+### BAM File
+This is the set of read alignments from the [ENCODE Project][encode-project] (`ENCFF205TSU.bam`). 
+
+<Link
+ className="button button--secondary"
+ href="https://www.encodeproject.org/files/ENCFF205TSU/@@download/ENCFF205TSU">
+ Download sample BAM file
+</Link>
+
+<br />
+<br />
+
+:::caution
+The BAM file is ~2.5GB large so make sure you have enough space on your machine before downloading.
+:::
+
+## Peak Calling ATAC-seq with MACS2 
+
+### 1. Install MACS2
+There are two common ways to install bioinformatics software: **pip** and **conda**.
+
+- **pip**: the Python package manager. It installs Python-based tools (like MACS2) into your environment. 
+- **conda**: an environment manager that can install packages (both Python and non-Python) with all dependencies. Widely used in bioinformatics. We’ll show both methods,
+
+#### 1.1 Install using pip 
+
+```bash
+# Create a clean Python environment 
+python3 -m venv macs2_env
+source macs2_env/bin/activate
+
+# Update pip and install MACS2
+pip install --upgrade pip wheel
+pip install numpy
+pip install MACS2
+```
+
+#### 1.2 Install using conda
+
+```bash
+conda create -n macs2_env python=3.8
+conda activate macs2_env
+conda install -c bioconda macs2
+```
+
+### 2. Generate BAI index file
+A BAI index file is required for each BAM file of interest (i.e., the tag occupancy data you want to plot). This file allows for rapid access of the sorted and aligned sequence reads (BAM file).
+
+:::tip
+
+SAM/BAM standard is to keep BAI file in same directory as BAM file with the ScriptManager-generated filename.
+
+```bash
+samtools index ENCFF205TSU.bam 
+```
+
+### 3. Run MACS2 for ATAC-seq
+ATAC-seq is slightly different from ChIP-seq because fragments are shifted by Tn5 transposase insertions and you usually call peaks with paired-end BAM.
+
+ ```bash
+ macs2 callpeak -t ENCFF205TSU.bam \
+ -f BAMPE \
+ -g hs \
+ -n sample_ATAC \
+ --outdir macs2_output \
+ --shift -100 --extsize 200 \
+ -q 0.01
+ ```
+
+ Key flags explained:
+ - -f BAMPE: Paired-end BAM input
+ - -g hs: Human genome
+ - --shift -100 --extsize 200: Adjusts for Tn5 integration offset
+ - -q 0.01: False Discovery Rate Threshold
+
+ The output files should be the follwoing: 
+ - **sample_ATAC_peaks.narrowPeak**: Peak regions (main file to use downstream) 
+ - **sample_ATAC_peaks.xls**: Detailed peak statistics
+ - **sample_ATAC_summits.bed**: Summit positions
+
+ ### 4. Convert 'sample_ATAC_peaks.narrowPeak' file to BED File
+
+```bash
+ cd macs2_output
+ cut -f1-3 sample_ATAC_peaks.narrowPeak > sample_ATAC_peaks.bed
+ awk '{print $1"\t"$2-1000"\t"$2+1000}' sample_ATAC_top1000_summits.bed > summits_1000bp.bed
+```
+
+ :::note
+ The file of this BED file is very large, so we use 1000bp to around each summit in order reduce processing time. 
+ :::
+
+ The output file should be the follwoing: 
+ - **sample_ATAC_peaks.bed**
+
+ ### 5. ScriptManager for TagPileup
+ScriptManager can plot composite pileups and heatmaps using BAM + BED.
+
+ ##### 5.1 Index Bam File: BAM Manipulation ➡️ [__BAM-BAI Indexer__][bam-indexer]
+```bash
+ ENCFF205TSU.bam
+ ENCFF205TSU.bam.bai # Need to generate this file to proceed.
+```
+:::
+
+<div class="tutorial-img-flow-container">
+ <img src={require('./img/bam_atacseq_peakcalling.png').default} style={{width:60+'%',}}/>
+ <i class="fa-solid fa-arrow-right fa-lg"></i>
+ <img src={require('./img/gui-bamidx-complete.png').default} style={{width:30+'%',}}/>
+</div>
+
+:::note
+The speed of this step scales with the size of the BAM file. Generally this step 30 sec for a 100 MB BAM file but may take 1-2 min for a multi-GB BAM file.
+:::
+
+
+ #### 5.2 TagPileup: Sequence Read Analysis ➡️ [__Tag Pileup__][tag-pileup]
+Use **"Full Fragment"** in the top right, then select **"Combined"** color , **"Output Composite"**, **"CDT"**, and **"Output GZIP"**. Then, proceed to "Output Directory".
+
+<div class="tutorial-img-flow-container">
+ <img src={require('./img/atacseq_peak_tagpileup.png').default} style={{width:100+'%',}}/>
+</div>
+
+<div class="tutorial-img-flow-container">
+ <img src={require('./img/atacseq_peak_pileup.png').default} style={{width:100+'%',}}/>
+</div>
+
+
+ ### 6. ScriptManager for Heatmap
+
+ #### 6.1 Sort BED file by CDT file: Coordinate File Manipulation ➡️ [__Sort BED__][sort-bed]
+
+<div class="tutorial-img-flow-container">
+ <img src={require('./img/atacseq_peak_sortcdt.png').default} style={{width:100+'%',}}/>
+</div>
+
+
+#### 6.2 Heatmap: Figure Generation ➡️ [__Heat Map__][heatmap] and Figure Generation ➡️ [__Label Heatmaps__][label-heatmap]
+
+<div class="tutorial-img-flow-container">
+ <img src={require('./img/atacseq_pea_heatmapgen.png').default} style={{width:55+'%',}}/>
+ <i class="fa-solid fa-arrow-right fa-lg"></i>
+ <img src={require('./img/atacseq_peak_heatmap.png').default} style={{width:45+'%',}}/>
+</div>
+
+## Command-Line shell script for ScriptManager
+
+The following shell commands records the locations for a BED file, a BAM file, and the anticipated OUTPUT basename as environmental variables to derive the corresponding composite plot values and heatmaps. This can serve as a template for you to write out your own workflows as bash scripts that execute command-line style ScriptManager.
+
+```bash
+SCRIPTMANAGER=/path/to/ScriptManager.jar
+BEDFILE=/path/to/sample_ATAC_top1000_summits.bed
+BAMFILE=/path/to/ENCFF205TSU.bam
+OUTPUT=/path/to/myoutput
+
+samtools index $BAMFILE
+
+java -jar $SCRIPTMANAGER read-analysis tag-pileup --combined --full-fragment $OUTPUT\_1000bp.bed $BAMFILE -o $OUTPUT\_composite.out -M $OUTPUT\_matrix
+java -jar $SCRIPTMANAGER coordinate-manipulation sort-bed -c 1000 $OUTPUT\_1000bp.bed $OUTPUT\_matrix_combined.cdt -o $OUTPUT\_SORT
+java -jar $SCRIPTMANAGER figure-generation heatmap -p .95 --black $OUTPUT\_SORT.cdt -o $OUTPUT\_heatmap.png
+
+# Output files:
+# - /path/to/myoutput_composite.out
+# - /path/to/myoutput_matrix_combined.cdt
+# - /path/to/myoutput_SORT.bed
+# - /path/to/myoutput_SORT.cdt
+# - /path/to/myoutput_heatmap.png
+```
+
+[encode-project]: https://www.encodeproject.org/experiments/ENCFF205TSU
+
+
+
+
+
+
+
+
+
+
+
+
+

docs/Tutorials/PeakCalling/chipexo-pcalling-chexmix.md

@@ -0,0 +1,6 @@
+---
+id: chipexo-pcalling-chexmix
+title: "ChIP-exo Peak Calling (ChExMix)"
+sidebar_label: "ChIP-exo Peak Calling (ChExMix)"
+sidebar_position: 2
+---

docs/Tutorials/PeakCalling/chipexo-pcalling-genetrack.md

@@ -0,0 +1,6 @@
+---
+id: chipexo-pcalling-genetrack
+title: "ChIP-exo Peak Calling (Genetrack/CWPair)"
+sidebar_label: "ChIP-exo Peak Calling (Genetrack/CWPair)"
+sidebar_position: 1
+---

docs/Tutorials/PeakCalling/index.md

@@ -0,0 +1,5 @@
+---
+title: "Peak Calling"
+sidebar_label: "Peak Calling"
+sidebar_position: 3
+---

docs/Tutorials/PeakCalling/procap-pcalling-genetrack.md

@@ -0,0 +1 @@
+a

docs/Guides/Getting-Started/getting-started.md → docs/Guides/Getting-Started/index.md

@@ -1,8 +1,7 @@
 ---
-id: getting-started
 title: Getting Started
 sidebar_label: Getting Started
-slug: /
+sidebar_position: 1
 ---
 
 import Tabs from '@theme/Tabs';

docs/Tutorials/GenomeTracks/atacseq-gtracks-deeptools.md

@@ -0,0 +1,6 @@
+---
+id: atacseq-gtracks-deeptools
+title: "ATAC-seq Genome Tracks (Deeptools)"
+sidebar_label: "ATAC-seq Genome Tracks (Deeptools)"
+sidebar_position: 2
+---

docs/Tutorials/GenomeTracks/chipexo-gtracks-deeptools.md

@@ -0,0 +1,6 @@
+---
+id: chipexo-gtracks-deeptools
+title: "ChIP-exo Genome Tracks (Deeptools)"
+sidebar_label: "ChIP-exo Genome Tracks (Deeptools)"
+sidebar_position: 1
+---

docs/Guides/Tutorials/genome-tracks-tutorial.md → docs/Tutorials/GenomeTracks/custom-gtracks-scriptmanager.md

@@ -1,7 +1,8 @@
 ---
-id: genome-tracks-tutorial
-title: "Making Genome Tracks Tutorial"
-sidebar_label: "Genome Tracks (BigWig)"
+id: custom-gtracks-scriptmanager
+title: "Making Custom Genome Tracks Tutorial"
+sidebar_label: "Custom Tracks (ScriptManager/Kent Tools)"
+sidebar_position: 3
 ---
 
 import Tabs from '@theme/Tabs';
@@ -69,7 +70,7 @@ OR
 
 
 <div class="tutorial-img-flow-container">
- <img src={require('./img/download-yep-home.png').default} style={{width:60+'%'}} />
+ <img src={require('../QuickStart/img/download-yep-home.png').default} style={{width:60+'%'}} />
 </div>
 
 1. Navigate to [www.yeastepigenome.org][yep-stencil] and search for Reb1
@@ -78,8 +79,8 @@ OR
 4. Unzip the resulting file ‘12141_YEP.zip’ and inspect the contents of the new `12141_YEP` folder. It should contain a file called `12141_filtered.bam`.
 
 <div class="tutorial-img-flow-container">
- <img src={require('./img/download-yep-reb1.png').default} style={{width:50+'%'}} />
- <img src={require('./img/download-yep-reb1-metadata.png').default} style={{width:50+'%'}} />
+ <img src={require('../QuickStart/img/download-yep-reb1.png').default} style={{width:50+'%'}} />
+ <img src={require('../QuickStart/img/download-yep-reb1-metadata.png').default} style={{width:50+'%'}} />
 </div>
 
 ### XXXX.chrom.sizes Reference File

docs/Tutorials/GenomeTracks/index.md

@@ -0,0 +1,5 @@
+---
+title: "Making Genome Tracks"
+sidebar_label: "Genome Tracks"
+sidebar_position: 2
+---

docs/Tutorials/PeakCalling/atacseq-pcalling-macs.md

@@ -0,0 +1,232 @@
+---
+id: atacseq-pcalling-macs
+title: "ATAC-seq Peak Calling (MACS)"
+sidebar_label: "ATAC-seq Peak Calling (MACS)"
+sidebar_position: 3
+---
+
+import Tabs from '@theme/Tabs';
+import TabItem from '@theme/TabItem';
+import Link from '@docusaurus/Link';
+
+_Performing ATAC-seq peak calling with MACS2_ 
+
+**Goal:** This tutorial provides a guide to peak calling using MACS2 and data generated by the [Stanford Encode Project][encode-project]. 
+
+---
+
+## Background
+
+### What is MACS2?
+**MACS2 (Model-based Analysis of ChIP-Seq)** is a widely used program to detect **peaks** — enriched regions in sequencing data where reads pile up. 
+- For **ChIP-seq**, peaks correspond to transcription factor binding sites. 
+- For **ATAC-seq**, peaks correspond to **open chromatin regions** cut by the Tn5 transposase. 
+
+That’s why we use MACS2 for ATAC-seq: it helps us identify the regions of the genome that are likely regulatory hotspots.
+
+---
+## Download Data
+
+You need one set of genomic coordinate regions to investigate (BED) and one file of sequencing data alignments (BAM) to complete this exercise. [Read more about the BED/BAM file formats here.][file-formats]
+
+
+### BED File
+This is the set of transcription start site (TSS) annotations for the GRCh38 genome build that has been subsampled down to 2000 sites for quick tutorial purposes. A more formal analysis may use a more complete set of annotations (many more sites).
+
+<Link
+ className="button button--secondary"
+ target="\_blank"
+ href="/sample_data/atac-seq-tutorial/UCSC_GRCh38_knownGene_GENCODEV3_TSS_2000bp_SUBSAMPLE-2000-Sites.bed" >
+ Download sample BED file
+</Link>
+
+<br />
+<br />
+
+:::caution
+If your BED file downloads with a `.txt` extension, make sure to change the filename to a `.bed` extension. For this tutorial, the BED file is named `UCSC_GRCh38_knownGene_GENCODEV3_TSS_2000bp_SUBSAMPLE-2000-Sites.bed`.
+:::
+
+### BAM File
+This is the set of read alignments from the [ENCODE Project][encode-project] (`ENCFF205TSU.bam`). 
+
+<Link
+ className="button button--secondary"
+ href="https://www.encodeproject.org/files/ENCFF205TSU/@@download/ENCFF205TSU">
+ Download sample BAM file
+</Link>
+
+<br />
+<br />
+
+:::caution
+The BAM file is ~2.5GB large so make sure you have enough space on your machine before downloading.
+:::
+
+## Peak Calling ATAC-seq with MACS2 
+
+### 1. Install MACS2
+There are two common ways to install bioinformatics software: **pip** and **conda**.
+
+- **pip**: the Python package manager. It installs Python-based tools (like MACS2) into your environment. 
+- **conda**: an environment manager that can install packages (both Python and non-Python) with all dependencies. Widely used in bioinformatics. We’ll show both methods,
+
+#### 1.1 Install using pip 
+
+```bash
+# Create a clean Python environment 
+python3 -m venv macs2_env
+source macs2_env/bin/activate
+
+# Update pip and install MACS2
+pip install --upgrade pip wheel
+pip install numpy
+pip install MACS2
+```
+
+#### 1.2 Install using conda
+
+```bash
+conda create -n macs2_env python=3.8
+conda activate macs2_env
+conda install -c bioconda macs2
+```
+
+### 2. Generate BAI index file
+A BAI index file is required for each BAM file of interest (i.e., the tag occupancy data you want to plot). This file allows for rapid access of the sorted and aligned sequence reads (BAM file).
+
+:::tip
+
+SAM/BAM standard is to keep BAI file in same directory as BAM file with the ScriptManager-generated filename.
+
+```bash
+samtools index ENCFF205TSU.bam 
+```
+
+### 3. Run MACS2 for ATAC-seq
+ATAC-seq is slightly different from ChIP-seq because fragments are shifted by Tn5 transposase insertions and you usually call peaks with paired-end BAM.
+
+ ```bash
+ macs2 callpeak -t ENCFF205TSU.bam \
+ -f BAMPE \
+ -g hs \
+ -n sample_ATAC \
+ --outdir macs2_output \
+ --shift -100 --extsize 200 \
+ -q 0.01
+ ```
+
+ Key flags explained:
+ - -f BAMPE: Paired-end BAM input
+ - -g hs: Human genome
+ - --shift -100 --extsize 200: Adjusts for Tn5 integration offset
+ - -q 0.01: False Discovery Rate Threshold
+
+ The output files should be the follwoing: 
+ - **sample_ATAC_peaks.narrowPeak**: Peak regions (main file to use downstream) 
+ - **sample_ATAC_peaks.xls**: Detailed peak statistics
+ - **sample_ATAC_summits.bed**: Summit positions
+
+ ### 4. Convert 'sample_ATAC_peaks.narrowPeak' file to BED File
+
+```bash
+ cd macs2_output
+ cut -f1-3 sample_ATAC_peaks.narrowPeak > sample_ATAC_peaks.bed
+ awk '{print $1"\t"$2-1000"\t"$2+1000}' sample_ATAC_top1000_summits.bed > summits_1000bp.bed
+```
+
+ :::note
+ The file of this BED file is very large, so we use 1000bp to around each summit in order reduce processing time. 
+ :::
+
+ The output file should be the follwoing: 
+ - **sample_ATAC_peaks.bed**
+
+ ### 5. ScriptManager for TagPileup
+ScriptManager can plot composite pileups and heatmaps using BAM + BED.
+
+ ##### 5.1 Index Bam File: BAM Manipulation ➡️ [__BAM-BAI Indexer__][bam-indexer]
+```bash
+ ENCFF205TSU.bam
+ ENCFF205TSU.bam.bai # Need to generate this file to proceed.
+```
+:::
+
+<div class="tutorial-img-flow-container">
+ <img src={require('./img/bam_atacseq_peakcalling.png').default} style={{width:60+'%',}}/>
+ <i class="fa-solid fa-arrow-right fa-lg"></i>
+ <img src={require('./img/gui-bamidx-complete.png').default} style={{width:30+'%',}}/>
+</div>
+
+:::note
+The speed of this step scales with the size of the BAM file. Generally this step 30 sec for a 100 MB BAM file but may take 1-2 min for a multi-GB BAM file.
+:::
+
+
+ #### 5.2 TagPileup: Sequence Read Analysis ➡️ [__Tag Pileup__][tag-pileup]
+Use **"Full Fragment"** in the top right, then select **"Combined"** color , **"Output Composite"**, **"CDT"**, and **"Output GZIP"**. Then, proceed to "Output Directory".
+
+<div class="tutorial-img-flow-container">
+ <img src={require('./img/atacseq_peak_tagpileup.png').default} style={{width:100+'%',}}/>
+</div>
+
+<div class="tutorial-img-flow-container">
+ <img src={require('./img/atacseq_peak_pileup.png').default} style={{width:100+'%',}}/>
+</div>
+
+
+ ### 6. ScriptManager for Heatmap
+
+ #### 6.1 Sort BED file by CDT file: Coordinate File Manipulation ➡️ [__Sort BED__][sort-bed]
+
+<div class="tutorial-img-flow-container">
+ <img src={require('./img/atacseq_peak_sortcdt.png').default} style={{width:100+'%',}}/>
+</div>
+
+
+#### 6.2 Heatmap: Figure Generation ➡️ [__Heat Map__][heatmap] and Figure Generation ➡️ [__Label Heatmaps__][label-heatmap]
+
+<div class="tutorial-img-flow-container">
+ <img src={require('./img/atacseq_pea_heatmapgen.png').default} style={{width:55+'%',}}/>
+ <i class="fa-solid fa-arrow-right fa-lg"></i>
+ <img src={require('./img/atacseq_peak_heatmap.png').default} style={{width:45+'%',}}/>
+</div>
+
+## Command-Line shell script for ScriptManager
+
+The following shell commands records the locations for a BED file, a BAM file, and the anticipated OUTPUT basename as environmental variables to derive the corresponding composite plot values and heatmaps. This can serve as a template for you to write out your own workflows as bash scripts that execute command-line style ScriptManager.
+
+```bash
+SCRIPTMANAGER=/path/to/ScriptManager.jar
+BEDFILE=/path/to/sample_ATAC_top1000_summits.bed
+BAMFILE=/path/to/ENCFF205TSU.bam
+OUTPUT=/path/to/myoutput
+
+samtools index $BAMFILE
+
+java -jar $SCRIPTMANAGER read-analysis tag-pileup --combined --full-fragment $OUTPUT\_1000bp.bed $BAMFILE -o $OUTPUT\_composite.out -M $OUTPUT\_matrix
+java -jar $SCRIPTMANAGER coordinate-manipulation sort-bed -c 1000 $OUTPUT\_1000bp.bed $OUTPUT\_matrix_combined.cdt -o $OUTPUT\_SORT
+java -jar $SCRIPTMANAGER figure-generation heatmap -p .95 --black $OUTPUT\_SORT.cdt -o $OUTPUT\_heatmap.png
+
+# Output files:
+# - /path/to/myoutput_composite.out
+# - /path/to/myoutput_matrix_combined.cdt
+# - /path/to/myoutput_SORT.bed
+# - /path/to/myoutput_SORT.cdt
+# - /path/to/myoutput_heatmap.png
+```
+
+[encode-project]: https://www.encodeproject.org/experiments/ENCFF205TSU
+
+
+
+
+
+
+
+
+
+
+
+
+

docs/Tutorials/PeakCalling/chipexo-pcalling-chexmix.md

@@ -0,0 +1,6 @@
+---
+id: chipexo-pcalling-chexmix
+title: "ChIP-exo Peak Calling (ChExMix)"
+sidebar_label: "ChIP-exo Peak Calling (ChExMix)"
+sidebar_position: 2
+---

docs/Tutorials/PeakCalling/chipexo-pcalling-genetrack.md

@@ -0,0 +1,6 @@
+---
+id: chipexo-pcalling-genetrack
+title: "ChIP-exo Peak Calling (Genetrack/CWPair)"
+sidebar_label: "ChIP-exo Peak Calling (Genetrack/CWPair)"
+sidebar_position: 1
+---

docs/Tutorials/PeakCalling/index.md

@@ -0,0 +1,5 @@
+---
+title: "Peak Calling"
+sidebar_label: "Peak Calling"
+sidebar_position: 3
+---

docs/Tutorials/PeakCalling/procap-pcalling-genetrack.md

@@ -0,0 +1 @@
+a

docs/Guides/Getting-Started/getting-started.md → docs/Guides/Getting-Started/index.md

@@ -1,8 +1,7 @@
 ---
-id: getting-started
 title: Getting Started
 sidebar_label: Getting Started
-slug: /
+sidebar_position: 1
 ---
 
 import Tabs from '@theme/Tabs';

docs/Tutorials/GenomeTracks/atacseq-gtracks-deeptools.md

@@ -0,0 +1,6 @@
+---
+id: atacseq-gtracks-deeptools
+title: "ATAC-seq Genome Tracks (Deeptools)"
+sidebar_label: "ATAC-seq Genome Tracks (Deeptools)"
+sidebar_position: 2
+---

docs/Tutorials/GenomeTracks/chipexo-gtracks-deeptools.md

@@ -0,0 +1,6 @@
+---
+id: chipexo-gtracks-deeptools
+title: "ChIP-exo Genome Tracks (Deeptools)"
+sidebar_label: "ChIP-exo Genome Tracks (Deeptools)"
+sidebar_position: 1
+---

docs/Guides/Tutorials/genome-tracks-tutorial.md → docs/Tutorials/GenomeTracks/custom-gtracks-scriptmanager.md

@@ -1,7 +1,8 @@
 ---
-id: genome-tracks-tutorial
-title: "Making Genome Tracks Tutorial"
-sidebar_label: "Genome Tracks (BigWig)"
+id: custom-gtracks-scriptmanager
+title: "Making Custom Genome Tracks Tutorial"
+sidebar_label: "Custom Tracks (ScriptManager/Kent Tools)"
+sidebar_position: 3
 ---
 
 import Tabs from '@theme/Tabs';
@@ -69,7 +70,7 @@ OR
 
 
 <div class="tutorial-img-flow-container">
- <img src={require('./img/download-yep-home.png').default} style={{width:60+'%'}} />
+ <img src={require('../QuickStart/img/download-yep-home.png').default} style={{width:60+'%'}} />
 </div>
 
 1. Navigate to [www.yeastepigenome.org][yep-stencil] and search for Reb1
@@ -78,8 +79,8 @@ OR
 4. Unzip the resulting file ‘12141_YEP.zip’ and inspect the contents of the new `12141_YEP` folder. It should contain a file called `12141_filtered.bam`.
 
 <div class="tutorial-img-flow-container">
- <img src={require('./img/download-yep-reb1.png').default} style={{width:50+'%'}} />
- <img src={require('./img/download-yep-reb1-metadata.png').default} style={{width:50+'%'}} />
+ <img src={require('../QuickStart/img/download-yep-reb1.png').default} style={{width:50+'%'}} />
+ <img src={require('../QuickStart/img/download-yep-reb1-metadata.png').default} style={{width:50+'%'}} />
 </div>
 
 ### XXXX.chrom.sizes Reference File

docs/Tutorials/GenomeTracks/index.md

@@ -0,0 +1,5 @@
+---
+title: "Making Genome Tracks"
+sidebar_label: "Genome Tracks"
+sidebar_position: 2
+---

docs/Tutorials/PeakCalling/atacseq-pcalling-macs.md

@@ -0,0 +1,232 @@
+---
+id: atacseq-pcalling-macs
+title: "ATAC-seq Peak Calling (MACS)"
+sidebar_label: "ATAC-seq Peak Calling (MACS)"
+sidebar_position: 3
+---
+
+import Tabs from '@theme/Tabs';
+import TabItem from '@theme/TabItem';
+import Link from '@docusaurus/Link';
+
+_Performing ATAC-seq peak calling with MACS2_ 
+
+**Goal:** This tutorial provides a guide to peak calling using MACS2 and data generated by the [Stanford Encode Project][encode-project]. 
+
+---
+
+## Background
+
+### What is MACS2?
+**MACS2 (Model-based Analysis of ChIP-Seq)** is a widely used program to detect **peaks** — enriched regions in sequencing data where reads pile up. 
+- For **ChIP-seq**, peaks correspond to transcription factor binding sites. 
+- For **ATAC-seq**, peaks correspond to **open chromatin regions** cut by the Tn5 transposase. 
+
+That’s why we use MACS2 for ATAC-seq: it helps us identify the regions of the genome that are likely regulatory hotspots.
+
+---
+## Download Data
+
+You need one set of genomic coordinate regions to investigate (BED) and one file of sequencing data alignments (BAM) to complete this exercise. [Read more about the BED/BAM file formats here.][file-formats]
+
+
+### BED File
+This is the set of transcription start site (TSS) annotations for the GRCh38 genome build that has been subsampled down to 2000 sites for quick tutorial purposes. A more formal analysis may use a more complete set of annotations (many more sites).
+
+<Link
+ className="button button--secondary"
+ target="\_blank"
+ href="/sample_data/atac-seq-tutorial/UCSC_GRCh38_knownGene_GENCODEV3_TSS_2000bp_SUBSAMPLE-2000-Sites.bed" >
+ Download sample BED file
+</Link>
+
+<br />
+<br />
+
+:::caution
+If your BED file downloads with a `.txt` extension, make sure to change the filename to a `.bed` extension. For this tutorial, the BED file is named `UCSC_GRCh38_knownGene_GENCODEV3_TSS_2000bp_SUBSAMPLE-2000-Sites.bed`.
+:::
+
+### BAM File
+This is the set of read alignments from the [ENCODE Project][encode-project] (`ENCFF205TSU.bam`). 
+
+<Link
+ className="button button--secondary"
+ href="https://www.encodeproject.org/files/ENCFF205TSU/@@download/ENCFF205TSU">
+ Download sample BAM file
+</Link>
+
+<br />
+<br />
+
+:::caution
+The BAM file is ~2.5GB large so make sure you have enough space on your machine before downloading.
+:::
+
+## Peak Calling ATAC-seq with MACS2 
+
+### 1. Install MACS2
+There are two common ways to install bioinformatics software: **pip** and **conda**.
+
+- **pip**: the Python package manager. It installs Python-based tools (like MACS2) into your environment. 
+- **conda**: an environment manager that can install packages (both Python and non-Python) with all dependencies. Widely used in bioinformatics. We’ll show both methods,
+
+#### 1.1 Install using pip 
+
+```bash
+# Create a clean Python environment 
+python3 -m venv macs2_env
+source macs2_env/bin/activate
+
+# Update pip and install MACS2
+pip install --upgrade pip wheel
+pip install numpy
+pip install MACS2
+```
+
+#### 1.2 Install using conda
+
+```bash
+conda create -n macs2_env python=3.8
+conda activate macs2_env
+conda install -c bioconda macs2
+```
+
+### 2. Generate BAI index file
+A BAI index file is required for each BAM file of interest (i.e., the tag occupancy data you want to plot). This file allows for rapid access of the sorted and aligned sequence reads (BAM file).
+
+:::tip
+
+SAM/BAM standard is to keep BAI file in same directory as BAM file with the ScriptManager-generated filename.
+
+```bash
+samtools index ENCFF205TSU.bam 
+```
+
+### 3. Run MACS2 for ATAC-seq
+ATAC-seq is slightly different from ChIP-seq because fragments are shifted by Tn5 transposase insertions and you usually call peaks with paired-end BAM.
+
+ ```bash
+ macs2 callpeak -t ENCFF205TSU.bam \
+ -f BAMPE \
+ -g hs \
+ -n sample_ATAC \
+ --outdir macs2_output \
+ --shift -100 --extsize 200 \
+ -q 0.01
+ ```
+
+ Key flags explained:
+ - -f BAMPE: Paired-end BAM input
+ - -g hs: Human genome
+ - --shift -100 --extsize 200: Adjusts for Tn5 integration offset
+ - -q 0.01: False Discovery Rate Threshold
+
+ The output files should be the follwoing: 
+ - **sample_ATAC_peaks.narrowPeak**: Peak regions (main file to use downstream) 
+ - **sample_ATAC_peaks.xls**: Detailed peak statistics
+ - **sample_ATAC_summits.bed**: Summit positions
+
+ ### 4. Convert 'sample_ATAC_peaks.narrowPeak' file to BED File
+
+```bash
+ cd macs2_output
+ cut -f1-3 sample_ATAC_peaks.narrowPeak > sample_ATAC_peaks.bed
+ awk '{print $1"\t"$2-1000"\t"$2+1000}' sample_ATAC_top1000_summits.bed > summits_1000bp.bed
+```
+
+ :::note
+ The file of this BED file is very large, so we use 1000bp to around each summit in order reduce processing time. 
+ :::
+
+ The output file should be the follwoing: 
+ - **sample_ATAC_peaks.bed**
+
+ ### 5. ScriptManager for TagPileup
+ScriptManager can plot composite pileups and heatmaps using BAM + BED.
+
+ ##### 5.1 Index Bam File: BAM Manipulation ➡️ [__BAM-BAI Indexer__][bam-indexer]
+```bash
+ ENCFF205TSU.bam
+ ENCFF205TSU.bam.bai # Need to generate this file to proceed.
+```
+:::
+
+<div class="tutorial-img-flow-container">
+ <img src={require('./img/bam_atacseq_peakcalling.png').default} style={{width:60+'%',}}/>
+ <i class="fa-solid fa-arrow-right fa-lg"></i>
+ <img src={require('./img/gui-bamidx-complete.png').default} style={{width:30+'%',}}/>
+</div>
+
+:::note
+The speed of this step scales with the size of the BAM file. Generally this step 30 sec for a 100 MB BAM file but may take 1-2 min for a multi-GB BAM file.
+:::
+
+
+ #### 5.2 TagPileup: Sequence Read Analysis ➡️ [__Tag Pileup__][tag-pileup]
+Use **"Full Fragment"** in the top right, then select **"Combined"** color , **"Output Composite"**, **"CDT"**, and **"Output GZIP"**. Then, proceed to "Output Directory".
+
+<div class="tutorial-img-flow-container">
+ <img src={require('./img/atacseq_peak_tagpileup.png').default} style={{width:100+'%',}}/>
+</div>
+
+<div class="tutorial-img-flow-container">
+ <img src={require('./img/atacseq_peak_pileup.png').default} style={{width:100+'%',}}/>
+</div>
+
+
+ ### 6. ScriptManager for Heatmap
+
+ #### 6.1 Sort BED file by CDT file: Coordinate File Manipulation ➡️ [__Sort BED__][sort-bed]
+
+<div class="tutorial-img-flow-container">
+ <img src={require('./img/atacseq_peak_sortcdt.png').default} style={{width:100+'%',}}/>
+</div>
+
+
+#### 6.2 Heatmap: Figure Generation ➡️ [__Heat Map__][heatmap] and Figure Generation ➡️ [__Label Heatmaps__][label-heatmap]
+
+<div class="tutorial-img-flow-container">
+ <img src={require('./img/atacseq_pea_heatmapgen.png').default} style={{width:55+'%',}}/>
+ <i class="fa-solid fa-arrow-right fa-lg"></i>
+ <img src={require('./img/atacseq_peak_heatmap.png').default} style={{width:45+'%',}}/>
+</div>
+
+## Command-Line shell script for ScriptManager
+
+The following shell commands records the locations for a BED file, a BAM file, and the anticipated OUTPUT basename as environmental variables to derive the corresponding composite plot values and heatmaps. This can serve as a template for you to write out your own workflows as bash scripts that execute command-line style ScriptManager.
+
+```bash
+SCRIPTMANAGER=/path/to/ScriptManager.jar
+BEDFILE=/path/to/sample_ATAC_top1000_summits.bed
+BAMFILE=/path/to/ENCFF205TSU.bam
+OUTPUT=/path/to/myoutput
+
+samtools index $BAMFILE
+
+java -jar $SCRIPTMANAGER read-analysis tag-pileup --combined --full-fragment $OUTPUT\_1000bp.bed $BAMFILE -o $OUTPUT\_composite.out -M $OUTPUT\_matrix
+java -jar $SCRIPTMANAGER coordinate-manipulation sort-bed -c 1000 $OUTPUT\_1000bp.bed $OUTPUT\_matrix_combined.cdt -o $OUTPUT\_SORT
+java -jar $SCRIPTMANAGER figure-generation heatmap -p .95 --black $OUTPUT\_SORT.cdt -o $OUTPUT\_heatmap.png
+
+# Output files:
+# - /path/to/myoutput_composite.out
+# - /path/to/myoutput_matrix_combined.cdt
+# - /path/to/myoutput_SORT.bed
+# - /path/to/myoutput_SORT.cdt
+# - /path/to/myoutput_heatmap.png
+```
+
+[encode-project]: https://www.encodeproject.org/experiments/ENCFF205TSU
+
+
+
+
+
+
+
+
+
+
+
+
+

docs/Tutorials/PeakCalling/chipexo-pcalling-chexmix.md

@@ -0,0 +1,6 @@
+---
+id: chipexo-pcalling-chexmix
+title: "ChIP-exo Peak Calling (ChExMix)"
+sidebar_label: "ChIP-exo Peak Calling (ChExMix)"
+sidebar_position: 2
+---

docs/Tutorials/PeakCalling/chipexo-pcalling-genetrack.md

@@ -0,0 +1,6 @@
+---
+id: chipexo-pcalling-genetrack
+title: "ChIP-exo Peak Calling (Genetrack/CWPair)"
+sidebar_label: "ChIP-exo Peak Calling (Genetrack/CWPair)"
+sidebar_position: 1
+---

docs/Tutorials/PeakCalling/index.md

@@ -0,0 +1,5 @@
+---
+title: "Peak Calling"
+sidebar_label: "Peak Calling"
+sidebar_position: 3
+---

docs/Tutorials/PeakCalling/procap-pcalling-genetrack.md

@@ -0,0 +1 @@
+a

docs/Guides/Getting-Started/getting-started.md → docs/Guides/Getting-Started/index.md

@@ -1,8 +1,7 @@
 ---
-id: getting-started
 title: Getting Started
 sidebar_label: Getting Started
-slug: /
+sidebar_position: 1
 ---
 
 import Tabs from '@theme/Tabs';

docs/Tutorials/GenomeTracks/atacseq-gtracks-deeptools.md

@@ -0,0 +1,6 @@
+---
+id: atacseq-gtracks-deeptools
+title: "ATAC-seq Genome Tracks (Deeptools)"
+sidebar_label: "ATAC-seq Genome Tracks (Deeptools)"
+sidebar_position: 2
+---

docs/Tutorials/GenomeTracks/chipexo-gtracks-deeptools.md

@@ -0,0 +1,6 @@
+---
+id: chipexo-gtracks-deeptools
+title: "ChIP-exo Genome Tracks (Deeptools)"
+sidebar_label: "ChIP-exo Genome Tracks (Deeptools)"
+sidebar_position: 1
+---

docs/Guides/Tutorials/genome-tracks-tutorial.md → docs/Tutorials/GenomeTracks/custom-gtracks-scriptmanager.md

@@ -1,7 +1,8 @@
 ---
-id: genome-tracks-tutorial
-title: "Making Genome Tracks Tutorial"
-sidebar_label: "Genome Tracks (BigWig)"
+id: custom-gtracks-scriptmanager
+title: "Making Custom Genome Tracks Tutorial"
+sidebar_label: "Custom Tracks (ScriptManager/Kent Tools)"
+sidebar_position: 3
 ---
 
 import Tabs from '@theme/Tabs';
@@ -69,7 +70,7 @@ OR
 
 
 <div class="tutorial-img-flow-container">
- <img src={require('./img/download-yep-home.png').default} style={{width:60+'%'}} />
+ <img src={require('../QuickStart/img/download-yep-home.png').default} style={{width:60+'%'}} />
 </div>
 
 1. Navigate to [www.yeastepigenome.org][yep-stencil] and search for Reb1
@@ -78,8 +79,8 @@ OR
 4. Unzip the resulting file ‘12141_YEP.zip’ and inspect the contents of the new `12141_YEP` folder. It should contain a file called `12141_filtered.bam`.
 
 <div class="tutorial-img-flow-container">
- <img src={require('./img/download-yep-reb1.png').default} style={{width:50+'%'}} />
- <img src={require('./img/download-yep-reb1-metadata.png').default} style={{width:50+'%'}} />
+ <img src={require('../QuickStart/img/download-yep-reb1.png').default} style={{width:50+'%'}} />
+ <img src={require('../QuickStart/img/download-yep-reb1-metadata.png').default} style={{width:50+'%'}} />
 </div>
 
 ### XXXX.chrom.sizes Reference File

docs/Tutorials/GenomeTracks/index.md

@@ -0,0 +1,5 @@
+---
+title: "Making Genome Tracks"
+sidebar_label: "Genome Tracks"
+sidebar_position: 2
+---

docs/Tutorials/PeakCalling/atacseq-pcalling-macs.md

@@ -0,0 +1,232 @@
+---
+id: atacseq-pcalling-macs
+title: "ATAC-seq Peak Calling (MACS)"
+sidebar_label: "ATAC-seq Peak Calling (MACS)"
+sidebar_position: 3
+---
+
+import Tabs from '@theme/Tabs';
+import TabItem from '@theme/TabItem';
+import Link from '@docusaurus/Link';
+
+_Performing ATAC-seq peak calling with MACS2_ 
+
+**Goal:** This tutorial provides a guide to peak calling using MACS2 and data generated by the [Stanford Encode Project][encode-project]. 
+
+---
+
+## Background
+
+### What is MACS2?
+**MACS2 (Model-based Analysis of ChIP-Seq)** is a widely used program to detect **peaks** — enriched regions in sequencing data where reads pile up. 
+- For **ChIP-seq**, peaks correspond to transcription factor binding sites. 
+- For **ATAC-seq**, peaks correspond to **open chromatin regions** cut by the Tn5 transposase. 
+
+That’s why we use MACS2 for ATAC-seq: it helps us identify the regions of the genome that are likely regulatory hotspots.
+
+---
+## Download Data
+
+You need one set of genomic coordinate regions to investigate (BED) and one file of sequencing data alignments (BAM) to complete this exercise. [Read more about the BED/BAM file formats here.][file-formats]
+
+
+### BED File
+This is the set of transcription start site (TSS) annotations for the GRCh38 genome build that has been subsampled down to 2000 sites for quick tutorial purposes. A more formal analysis may use a more complete set of annotations (many more sites).
+
+<Link
+ className="button button--secondary"
+ target="\_blank"
+ href="/sample_data/atac-seq-tutorial/UCSC_GRCh38_knownGene_GENCODEV3_TSS_2000bp_SUBSAMPLE-2000-Sites.bed" >
+ Download sample BED file
+</Link>
+
+<br />
+<br />
+
+:::caution
+If your BED file downloads with a `.txt` extension, make sure to change the filename to a `.bed` extension. For this tutorial, the BED file is named `UCSC_GRCh38_knownGene_GENCODEV3_TSS_2000bp_SUBSAMPLE-2000-Sites.bed`.
+:::
+
+### BAM File
+This is the set of read alignments from the [ENCODE Project][encode-project] (`ENCFF205TSU.bam`). 
+
+<Link
+ className="button button--secondary"
+ href="https://www.encodeproject.org/files/ENCFF205TSU/@@download/ENCFF205TSU">
+ Download sample BAM file
+</Link>
+
+<br />
+<br />
+
+:::caution
+The BAM file is ~2.5GB large so make sure you have enough space on your machine before downloading.
+:::
+
+## Peak Calling ATAC-seq with MACS2 
+
+### 1. Install MACS2
+There are two common ways to install bioinformatics software: **pip** and **conda**.
+
+- **pip**: the Python package manager. It installs Python-based tools (like MACS2) into your environment. 
+- **conda**: an environment manager that can install packages (both Python and non-Python) with all dependencies. Widely used in bioinformatics. We’ll show both methods,
+
+#### 1.1 Install using pip 
+
+```bash
+# Create a clean Python environment 
+python3 -m venv macs2_env
+source macs2_env/bin/activate
+
+# Update pip and install MACS2
+pip install --upgrade pip wheel
+pip install numpy
+pip install MACS2
+```
+
+#### 1.2 Install using conda
+
+```bash
+conda create -n macs2_env python=3.8
+conda activate macs2_env
+conda install -c bioconda macs2
+```
+
+### 2. Generate BAI index file
+A BAI index file is required for each BAM file of interest (i.e., the tag occupancy data you want to plot). This file allows for rapid access of the sorted and aligned sequence reads (BAM file).
+
+:::tip
+
+SAM/BAM standard is to keep BAI file in same directory as BAM file with the ScriptManager-generated filename.
+
+```bash
+samtools index ENCFF205TSU.bam 
+```
+
+### 3. Run MACS2 for ATAC-seq
+ATAC-seq is slightly different from ChIP-seq because fragments are shifted by Tn5 transposase insertions and you usually call peaks with paired-end BAM.
+
+ ```bash
+ macs2 callpeak -t ENCFF205TSU.bam \
+ -f BAMPE \
+ -g hs \
+ -n sample_ATAC \
+ --outdir macs2_output \
+ --shift -100 --extsize 200 \
+ -q 0.01
+ ```
+
+ Key flags explained:
+ - -f BAMPE: Paired-end BAM input
+ - -g hs: Human genome
+ - --shift -100 --extsize 200: Adjusts for Tn5 integration offset
+ - -q 0.01: False Discovery Rate Threshold
+
+ The output files should be the follwoing: 
+ - **sample_ATAC_peaks.narrowPeak**: Peak regions (main file to use downstream) 
+ - **sample_ATAC_peaks.xls**: Detailed peak statistics
+ - **sample_ATAC_summits.bed**: Summit positions
+
+ ### 4. Convert 'sample_ATAC_peaks.narrowPeak' file to BED File
+
+```bash
+ cd macs2_output
+ cut -f1-3 sample_ATAC_peaks.narrowPeak > sample_ATAC_peaks.bed
+ awk '{print $1"\t"$2-1000"\t"$2+1000}' sample_ATAC_top1000_summits.bed > summits_1000bp.bed
+```
+
+ :::note
+ The file of this BED file is very large, so we use 1000bp to around each summit in order reduce processing time. 
+ :::
+
+ The output file should be the follwoing: 
+ - **sample_ATAC_peaks.bed**
+
+ ### 5. ScriptManager for TagPileup
+ScriptManager can plot composite pileups and heatmaps using BAM + BED.
+
+ ##### 5.1 Index Bam File: BAM Manipulation ➡️ [__BAM-BAI Indexer__][bam-indexer]
+```bash
+ ENCFF205TSU.bam
+ ENCFF205TSU.bam.bai # Need to generate this file to proceed.
+```
+:::
+
+<div class="tutorial-img-flow-container">
+ <img src={require('./img/bam_atacseq_peakcalling.png').default} style={{width:60+'%',}}/>
+ <i class="fa-solid fa-arrow-right fa-lg"></i>
+ <img src={require('./img/gui-bamidx-complete.png').default} style={{width:30+'%',}}/>
+</div>
+
+:::note
+The speed of this step scales with the size of the BAM file. Generally this step 30 sec for a 100 MB BAM file but may take 1-2 min for a multi-GB BAM file.
+:::
+
+
+ #### 5.2 TagPileup: Sequence Read Analysis ➡️ [__Tag Pileup__][tag-pileup]
+Use **"Full Fragment"** in the top right, then select **"Combined"** color , **"Output Composite"**, **"CDT"**, and **"Output GZIP"**. Then, proceed to "Output Directory".
+
+<div class="tutorial-img-flow-container">
+ <img src={require('./img/atacseq_peak_tagpileup.png').default} style={{width:100+'%',}}/>
+</div>
+
+<div class="tutorial-img-flow-container">
+ <img src={require('./img/atacseq_peak_pileup.png').default} style={{width:100+'%',}}/>
+</div>
+
+
+ ### 6. ScriptManager for Heatmap
+
+ #### 6.1 Sort BED file by CDT file: Coordinate File Manipulation ➡️ [__Sort BED__][sort-bed]
+
+<div class="tutorial-img-flow-container">
+ <img src={require('./img/atacseq_peak_sortcdt.png').default} style={{width:100+'%',}}/>
+</div>
+
+
+#### 6.2 Heatmap: Figure Generation ➡️ [__Heat Map__][heatmap] and Figure Generation ➡️ [__Label Heatmaps__][label-heatmap]
+
+<div class="tutorial-img-flow-container">
+ <img src={require('./img/atacseq_pea_heatmapgen.png').default} style={{width:55+'%',}}/>
+ <i class="fa-solid fa-arrow-right fa-lg"></i>
+ <img src={require('./img/atacseq_peak_heatmap.png').default} style={{width:45+'%',}}/>
+</div>
+
+## Command-Line shell script for ScriptManager
+
+The following shell commands records the locations for a BED file, a BAM file, and the anticipated OUTPUT basename as environmental variables to derive the corresponding composite plot values and heatmaps. This can serve as a template for you to write out your own workflows as bash scripts that execute command-line style ScriptManager.
+
+```bash
+SCRIPTMANAGER=/path/to/ScriptManager.jar
+BEDFILE=/path/to/sample_ATAC_top1000_summits.bed
+BAMFILE=/path/to/ENCFF205TSU.bam
+OUTPUT=/path/to/myoutput
+
+samtools index $BAMFILE
+
+java -jar $SCRIPTMANAGER read-analysis tag-pileup --combined --full-fragment $OUTPUT\_1000bp.bed $BAMFILE -o $OUTPUT\_composite.out -M $OUTPUT\_matrix
+java -jar $SCRIPTMANAGER coordinate-manipulation sort-bed -c 1000 $OUTPUT\_1000bp.bed $OUTPUT\_matrix_combined.cdt -o $OUTPUT\_SORT
+java -jar $SCRIPTMANAGER figure-generation heatmap -p .95 --black $OUTPUT\_SORT.cdt -o $OUTPUT\_heatmap.png
+
+# Output files:
+# - /path/to/myoutput_composite.out
+# - /path/to/myoutput_matrix_combined.cdt
+# - /path/to/myoutput_SORT.bed
+# - /path/to/myoutput_SORT.cdt
+# - /path/to/myoutput_heatmap.png
+```
+
+[encode-project]: https://www.encodeproject.org/experiments/ENCFF205TSU
+
+
+
+
+
+
+
+
+
+
+
+
+

docs/Tutorials/PeakCalling/chipexo-pcalling-chexmix.md

@@ -0,0 +1,6 @@
+---
+id: chipexo-pcalling-chexmix
+title: "ChIP-exo Peak Calling (ChExMix)"
+sidebar_label: "ChIP-exo Peak Calling (ChExMix)"
+sidebar_position: 2
+---

docs/Tutorials/PeakCalling/chipexo-pcalling-genetrack.md

@@ -0,0 +1,6 @@
+---
+id: chipexo-pcalling-genetrack
+title: "ChIP-exo Peak Calling (Genetrack/CWPair)"
+sidebar_label: "ChIP-exo Peak Calling (Genetrack/CWPair)"
+sidebar_position: 1
+---

docs/Tutorials/PeakCalling/index.md

@@ -0,0 +1,5 @@
+---
+title: "Peak Calling"
+sidebar_label: "Peak Calling"
+sidebar_position: 3
+---

docs/Tutorials/PeakCalling/procap-pcalling-genetrack.md

@@ -0,0 +1 @@
+a