Nextflow DSL2 pipeline for differential Alternative Splicing analysis using rMATS or SplAdder
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
- Specifies the tool you want to use in your analysis [rmats or spladder]
- 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)
- Specifies the name of the first group of samples you want to inlude in the analysis
- Specifies the name of the second group of samples you want to inlude in the analysis
- Specifies the path to the GTF file required for the analysis
- Specifies the path to the indexed bam files (.bai) required for the analysis