diff-AS-nf

Nextflow DSL2 pipeline for differential Alternative Splicing analysis using rMATS or SplAdder

Quick start

Make sure you have docker/singularity installed.

Install the Nextflow runtime by running the following command:

curl -fsSL get.nextflow.io | bash

You can launch the pipeline execution by entering the command shown below specifying the required parameters:

nextflow run athbaltzis/diff-AS-nf

Pipeline parameters

--tool

• Specifies the tool you want to use in your analysis [rmats or spladder]

--input_csv

• Specifies the input csv file that contains the information about the conditions of the samples and the paths of the bam files (see data/bams.csv)

--groupA

• Specifies the name of the first group of samples you want to inlude in the analysis

--groupB

• Specifies the name of the second group of samples you want to inlude in the analysis

--gtf

• Specifies the path to the GTF file required for the analysis

--bai

• Specifies the path to the indexed bam files (.bai) required for the analysis