RNA data can be used to call variants and/or for differential expression analysis. This repo contains bash scripts for running differential gene expression and variant calling.
- For variant calling, bash scripts for GATK Best practices workflow for variant calling using RNAseq data are provided.
- For differential gene expression analysis, Tophat2-HTSEQ/Featurecounts and Tophat2-Cufflinks-Cummerbund (Tuxedo suite protocol 1) scripts are provided. cummerbund R script is provided separate.
Please note that tuxedo suite protocol 1 not suggested, rather new tuxedo workflow HISAT2-StringTie-Ballgown, is preferred in place of existing protocol. New protocol is provided in another repository of mine, as a tuxedo 2 workflow written using snakemake library.