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ASEtrans

Codes for allele specific expression analysis

Two Perl scripts were provided to generate the transcriptome and genes list for RSEM.
get_allele_specific_transcripts.pl introduce variants from a VCF file into transcripts defined in one GFF file.
This code assumes that the variants have been phased, and stored as first record in "sample" fields of the VCF files.

get_geneID.pl generate the corresponding lists between allele IDs and transcripts IDs.

Usage:

Prepare vcf file:

/usr/local/tabix/latest/bin/bgzip xxx.vcf

/usr/local/tabix/latest/bin/tabix -p vcf xxx.vcf.gz

Get transcripts:
perl get_allele_specific_transcripts.pl --gff gff --genomefile genome --vcf vcf --out out

 vcf --> vcf data of hybrid sample
genome --> reference genome fasta file used to generate vcf file
This script requires Vcf.pm

Get gene list file:
perl get_geneID.pl --gff gff --out out

DEMO command line for RSEM

cd RSEM
/usr/local/rsem/latest/rsem-prepare-reference \
--transcript-to-gene-map P1979_gene_list.txt \
--bowtie2 --bowtie2-path /usr/local/bowtie2/latest/bin/ \
P1979_allele_trans.fasta ref/P1979_allele_ref &

/usr/local/rsem/latest/rsem-calculate-expression -p 5 --paired-end \
--bowtie2 --bowtie2-path /usr/local/bowtie2/latest/bin/ \
--estimate-rspd --bowtie2-mismatch-rate 0.2 \
RNAseq_R1.fq RNAseq_R2.fq \
ref/P1979_allele_ref exp/RNAseq_s1

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Codes for allele specific expression

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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
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}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

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ASEtrans
Codes for allele specific expression analysis
Two Perl scripts were provided to generate the transcriptome and genes list for RSEM.

get_allele_specific_transcripts.pl introduce variants from a VCF file into transcripts defined in one GFF file.

This code assumes that the variants have been phased, and stored as first record in "sample" fields of the VCF files.
get_geneID.pl generate the corresponding lists between allele IDs and transcripts IDs.
Usage:
Prepare vcf file:
/usr/local/tabix/latest/bin/bgzip xxx.vcf
/usr/local/tabix/latest/bin/tabix -p vcf xxx.vcf.gz
Get transcripts:

perl get_allele_specific_transcripts.pl --gff gff --genomefile genome --vcf vcf --out out
 vcf --> vcf data of hybrid sample
genome --> reference genome fasta file used to generate vcf file
This script requires Vcf.pm

Get gene list file:

perl get_geneID.pl --gff gff --out out
DEMO command line for RSEM
cd RSEM

/usr/local/rsem/latest/rsem-prepare-reference \

--transcript-to-gene-map P1979_gene_list.txt \

--bowtie2 --bowtie2-path /usr/local/bowtie2/latest/bin/ \

P1979_allele_trans.fasta ref/P1979_allele_ref &
/usr/local/rsem/latest/rsem-calculate-expression -p 5 --paired-end \

--bowtie2 --bowtie2-path /usr/local/bowtie2/latest/bin/ \

--estimate-rspd --bowtie2-mismatch-rate 0.2 \

RNAseq_R1.fq RNAseq_R2.fq \

ref/P1979_allele_ref exp/RNAseq_s1
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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ASEtrans
Codes for allele specific expression analysis
Two Perl scripts were provided to generate the transcriptome and genes list for RSEM.

get_allele_specific_transcripts.pl introduce variants from a VCF file into transcripts defined in one GFF file.

This code assumes that the variants have been phased, and stored as first record in "sample" fields of the VCF files.
get_geneID.pl generate the corresponding lists between allele IDs and transcripts IDs.
Usage:
Prepare vcf file:
/usr/local/tabix/latest/bin/bgzip xxx.vcf
/usr/local/tabix/latest/bin/tabix -p vcf xxx.vcf.gz
Get transcripts:

perl get_allele_specific_transcripts.pl --gff gff --genomefile genome --vcf vcf --out out
 vcf --> vcf data of hybrid sample
genome --> reference genome fasta file used to generate vcf file
This script requires Vcf.pm

Get gene list file:

perl get_geneID.pl --gff gff --out out
DEMO command line for RSEM
cd RSEM

/usr/local/rsem/latest/rsem-prepare-reference \

--transcript-to-gene-map P1979_gene_list.txt \

--bowtie2 --bowtie2-path /usr/local/bowtie2/latest/bin/ \

P1979_allele_trans.fasta ref/P1979_allele_ref &
/usr/local/rsem/latest/rsem-calculate-expression -p 5 --paired-end \

--bowtie2 --bowtie2-path /usr/local/bowtie2/latest/bin/ \

--estimate-rspd --bowtie2-mismatch-rate 0.2 \

RNAseq_R1.fq RNAseq_R2.fq \

ref/P1979_allele_ref exp/RNAseq_s1
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Codes for allele specific expression
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1 watching
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1 fork
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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ASEtrans
Codes for allele specific expression analysis
Two Perl scripts were provided to generate the transcriptome and genes list for RSEM.

get_allele_specific_transcripts.pl introduce variants from a VCF file into transcripts defined in one GFF file.

This code assumes that the variants have been phased, and stored as first record in "sample" fields of the VCF files.
get_geneID.pl generate the corresponding lists between allele IDs and transcripts IDs.
Usage:
Prepare vcf file:
/usr/local/tabix/latest/bin/bgzip xxx.vcf
/usr/local/tabix/latest/bin/tabix -p vcf xxx.vcf.gz
Get transcripts:

perl get_allele_specific_transcripts.pl --gff gff --genomefile genome --vcf vcf --out out
 vcf --> vcf data of hybrid sample
genome --> reference genome fasta file used to generate vcf file
This script requires Vcf.pm

Get gene list file:

perl get_geneID.pl --gff gff --out out
DEMO command line for RSEM
cd RSEM

/usr/local/rsem/latest/rsem-prepare-reference \

--transcript-to-gene-map P1979_gene_list.txt \

--bowtie2 --bowtie2-path /usr/local/bowtie2/latest/bin/ \

P1979_allele_trans.fasta ref/P1979_allele_ref &
/usr/local/rsem/latest/rsem-calculate-expression -p 5 --paired-end \

--bowtie2 --bowtie2-path /usr/local/bowtie2/latest/bin/ \

--estimate-rspd --bowtie2-mismatch-rate 0.2 \

RNAseq_R1.fq RNAseq_R2.fq \

ref/P1979_allele_ref exp/RNAseq_s1
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Codes for allele specific expression
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
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ASEtrans
Codes for allele specific expression analysis
Two Perl scripts were provided to generate the transcriptome and genes list for RSEM.

get_allele_specific_transcripts.pl introduce variants from a VCF file into transcripts defined in one GFF file.

This code assumes that the variants have been phased, and stored as first record in "sample" fields of the VCF files.
get_geneID.pl generate the corresponding lists between allele IDs and transcripts IDs.
Usage:
Prepare vcf file:
/usr/local/tabix/latest/bin/bgzip xxx.vcf
/usr/local/tabix/latest/bin/tabix -p vcf xxx.vcf.gz
Get transcripts:

perl get_allele_specific_transcripts.pl --gff gff --genomefile genome --vcf vcf --out out
 vcf --> vcf data of hybrid sample
genome --> reference genome fasta file used to generate vcf file
This script requires Vcf.pm

Get gene list file:

perl get_geneID.pl --gff gff --out out
DEMO command line for RSEM
cd RSEM

/usr/local/rsem/latest/rsem-prepare-reference \

--transcript-to-gene-map P1979_gene_list.txt \

--bowtie2 --bowtie2-path /usr/local/bowtie2/latest/bin/ \

P1979_allele_trans.fasta ref/P1979_allele_ref &
/usr/local/rsem/latest/rsem-calculate-expression -p 5 --paired-end \

--bowtie2 --bowtie2-path /usr/local/bowtie2/latest/bin/ \

--estimate-rspd --bowtie2-mismatch-rate 0.2 \

RNAseq_R1.fq RNAseq_R2.fq \

ref/P1979_allele_ref exp/RNAseq_s1
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Codes for allele specific expression
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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ASEtrans
Codes for allele specific expression analysis
Two Perl scripts were provided to generate the transcriptome and genes list for RSEM.

get_allele_specific_transcripts.pl introduce variants from a VCF file into transcripts defined in one GFF file.

This code assumes that the variants have been phased, and stored as first record in "sample" fields of the VCF files.
get_geneID.pl generate the corresponding lists between allele IDs and transcripts IDs.
Usage:
Prepare vcf file:
/usr/local/tabix/latest/bin/bgzip xxx.vcf
/usr/local/tabix/latest/bin/tabix -p vcf xxx.vcf.gz
Get transcripts:

perl get_allele_specific_transcripts.pl --gff gff --genomefile genome --vcf vcf --out out
 vcf --> vcf data of hybrid sample
genome --> reference genome fasta file used to generate vcf file
This script requires Vcf.pm

Get gene list file:

perl get_geneID.pl --gff gff --out out
DEMO command line for RSEM
cd RSEM

/usr/local/rsem/latest/rsem-prepare-reference \

--transcript-to-gene-map P1979_gene_list.txt \

--bowtie2 --bowtie2-path /usr/local/bowtie2/latest/bin/ \

P1979_allele_trans.fasta ref/P1979_allele_ref &
/usr/local/rsem/latest/rsem-calculate-expression -p 5 --paired-end \

--bowtie2 --bowtie2-path /usr/local/bowtie2/latest/bin/ \

--estimate-rspd --bowtie2-mismatch-rate 0.2 \

RNAseq_R1.fq RNAseq_R2.fq \

ref/P1979_allele_ref exp/RNAseq_s1
About
Codes for allele specific expression
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Watchers
1 watching
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1 fork
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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ASEtrans
Codes for allele specific expression analysis
Two Perl scripts were provided to generate the transcriptome and genes list for RSEM.

get_allele_specific_transcripts.pl introduce variants from a VCF file into transcripts defined in one GFF file.

This code assumes that the variants have been phased, and stored as first record in "sample" fields of the VCF files.
get_geneID.pl generate the corresponding lists between allele IDs and transcripts IDs.
Usage:
Prepare vcf file:
/usr/local/tabix/latest/bin/bgzip xxx.vcf
/usr/local/tabix/latest/bin/tabix -p vcf xxx.vcf.gz
Get transcripts:

perl get_allele_specific_transcripts.pl --gff gff --genomefile genome --vcf vcf --out out
 vcf --> vcf data of hybrid sample
genome --> reference genome fasta file used to generate vcf file
This script requires Vcf.pm

Get gene list file:

perl get_geneID.pl --gff gff --out out
DEMO command line for RSEM
cd RSEM

/usr/local/rsem/latest/rsem-prepare-reference \

--transcript-to-gene-map P1979_gene_list.txt \

--bowtie2 --bowtie2-path /usr/local/bowtie2/latest/bin/ \

P1979_allele_trans.fasta ref/P1979_allele_ref &
/usr/local/rsem/latest/rsem-calculate-expression -p 5 --paired-end \

--bowtie2 --bowtie2-path /usr/local/bowtie2/latest/bin/ \

--estimate-rspd --bowtie2-mismatch-rate 0.2 \

RNAseq_R1.fq RNAseq_R2.fq \

ref/P1979_allele_ref exp/RNAseq_s1
About
Codes for allele specific expression
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

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ASEtrans
Codes for allele specific expression analysis
Two Perl scripts were provided to generate the transcriptome and genes list for RSEM.

get_allele_specific_transcripts.pl introduce variants from a VCF file into transcripts defined in one GFF file.

This code assumes that the variants have been phased, and stored as first record in "sample" fields of the VCF files.
get_geneID.pl generate the corresponding lists between allele IDs and transcripts IDs.
Usage:
Prepare vcf file:
/usr/local/tabix/latest/bin/bgzip xxx.vcf
/usr/local/tabix/latest/bin/tabix -p vcf xxx.vcf.gz
Get transcripts:

perl get_allele_specific_transcripts.pl --gff gff --genomefile genome --vcf vcf --out out
 vcf --> vcf data of hybrid sample
genome --> reference genome fasta file used to generate vcf file
This script requires Vcf.pm

Get gene list file:

perl get_geneID.pl --gff gff --out out
DEMO command line for RSEM
cd RSEM

/usr/local/rsem/latest/rsem-prepare-reference \

--transcript-to-gene-map P1979_gene_list.txt \

--bowtie2 --bowtie2-path /usr/local/bowtie2/latest/bin/ \

P1979_allele_trans.fasta ref/P1979_allele_ref &
/usr/local/rsem/latest/rsem-calculate-expression -p 5 --paired-end \

--bowtie2 --bowtie2-path /usr/local/bowtie2/latest/bin/ \

--estimate-rspd --bowtie2-mismatch-rate 0.2 \

RNAseq_R1.fq RNAseq_R2.fq \

ref/P1979_allele_ref exp/RNAseq_s1
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Codes for allele specific expression
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