RNA-seq Pipeline for Mycobacterium tuberculosis

A basic RNA-sequencing pipeline for QC, alignment, and counting of paired-end reads generated by Illumina next gen sequencing for the Baughn Lab. This pipeline in its current iteration is meant to run through submission to the MSI Slurm queue as a single file and load all modules required directly from MSI.

Pipeline Summary

1. Quality Check (FastQc)
2. T-overhang trimming (Cutadapt)
3. rRNA contamination removal (ribodetector)
3. Alignment (STAR)
4. Counting (FeatureCounts)
5. QC (RSeQC)
6. Combine all outputs (MultiQC)

Usage

Running the pipeline

qsub RNAseq_Analysis.sh -f [/path/to/RNAseqfolder] -i [/path/to/inputfiledirectory] -d [/path/to/DNAreferences]

Dependencies

TBAdded

To Add

• Replace Cutadapt with package that runs faster and is more dynamic (Trimmomatic/Trim Galore!)

More extensive quality control with:

• BEDtools, bedGraphToBigWig
• Qualimap