This repository contains snakemake script for analyzing RNAseq samples from Griffith lab tutorial and data used in the tutorial is available here. This script follows Tuxedo2 protocol (HISAT2-STRINGTIE-BALLGOWN). Workflow has following steps:
- Quality check by fastqc
- Adapter trimming by cutadapt
- Quality check post adapter trimming by fastqc
- Alignment with HISAT2
- Transcript quanitification with Stringtie
- Statistical tests and visualization with Ballgown (in R)
Please note that this script is not production ready. This is for beginners in using snakemake. For generating graph, snakefile should be in sentence case.