RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.

These are tutorials on a subset of tools available for processing raw RNAseq data. This if for HISAT2_SAMtools_Stringtie_gffcompare_ballgown pipeline or HISAT2_SAMtools_Stringtie_PrepDEanalysis.py_DESeq2 pipeline

This project uses an workflow pipeline to generate map and assemble RNAseq reads to a reference genome. Furthermore, we generate counts data and identify differentially expressed genes from 2 conditions.