FastdRNA: a workflow for analysis of ONT direct RNA seq dataset

FastdRNA is a pipeline written in snakemake to handle ONT direct RNA seq database.

We have published a handbook which includes more details, please read FdRhandbook before using it!

The analysis includes :

• dRNAmain: a module for basecalling. mapping and transcript count.
• dRNAtail: a module for RNA poly(A) length estimate.
• dRNAmodif: a module for RNA modification detection.
• dRNAas: a module for alternative splicing analysis.

Installation

Users need to install snakemake and conda before.

Then you can download the workflow by:

git clone https://github.com/Tomcxf/FASTdRNA.git

Required software and relative dependence can be installed through conda by typing

conda env create -f environment.yml

There're two software need to install in binary file.

• a branch of nanopolish suitable for slow5

• f5c

Finally, for the reason that copyright protection, we can't supply Guppy directly. Searcher should download Guppy in Nanopore Comm

Usage

All workflow files and config templates live in script/, so run the commands from inside that folder (the config path is resolved relative to the working directory):

 cd script
 snakemake -s {dRNAmain.py / dRNAtail.py / dRNAmodif_1.py / dRNAmodif_2.py / dRNAas.py}
           -s the snakemake file you want to run
           --cores / -c : the number of cores to use (necessary)
           --set-threads myrule=XXX set threads XXX for running

tips

To generate a offical report by snakemake, users can run

snakemake --report report.html

after pipeline finished.

Citation

Chen X, Liu Y, Lv K, Wang M, Liu X, Li B. FASTdRNA: a workflow for the analysis of ONT direct RNA sequencing. Bioinform Adv. 2023 Jul 20;3(1):vbad099. doi: 10.1093/bioadv/vbad099. PMID: 37521311; PMCID: PMC10375421. link