rmats-nf:

A pipeline to retrieve RNA sequencing data from SRA, perform alignment with hisat2 and characterize splicing events with rMATS 3.2.5.

rmats-nf: Documentation

An overview of how the pipeline works, how to run it and a description of all of the different command-line flags.

Usage

The typical command for running the pipeline is as follows:

nextflow run lifebit-ai/rmats-nf --accessionList 'accession_list.txt' -profile docker

Mandatory arguments:

--accessionList

Path to input file with accession list to fetch from SRA

--gencodeFile

Path to input gencode GTF file

--keyFile

Path to a keyfile used to fetch restricted access datasets with SRAtools

-profile

Configuration profile to use. Can use multiple (comma separated) Available: short-test, key-test

Other arguments:

--skipTrimming

If used, trimming will be ommited.

--readType

Specifies what type of input reads are to be processed. Accepted values: single end, paired end

--readLength

Specifies the read length