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

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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.

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

Usage

 snakemake -s {dRNAmain.py / dRNAtail.py / dRNAmodif.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