Nexflow pipeline for RNA-seq experiment, currently implemented for use with SGE scheduler on HPC. Aligns reads to reference genome, obtains gene counts and perorms alternative splicing analysis.
Step 1: Performs QC with FASTQC and Trim_galore
Step 2: Aligns reads using Star and sorts with Samtools
Step 3: Obtains read counts for each sample using Featurecounts
Step 4: Merges reads counts for all samples for downstream analysis
Step 5 & 6: Creates config file for Majiq
Step 7: Performs Majiq build.
Step 8: Performs splicing analysis per sample using Majiq