deanpettinga / rnaseq_workflow

snakemake workflow for bulk RNA-seq workflow using STAR-edgeR

Sunflower Domestication RNAseq

Author

• Dean Pettinga @deanpettinga

Analysis Outline

1. prepare STAR indexes for Arikara and Nebraska

• copies corrected HanXRQr2 genomes into references/
• makes STAR indexes for each genome for alignments

2. raw read QC

• Trim_Galore on paired-end reads (min Quality =20)
• fastQC on each library

3. Alignment

• STAR alignment of adapter and quality-trimmed paired end libraries to reference genomes (arikara used for all domesticated samples, nebraska used for all wild samples)
  • output are BAM sorted by coordinates, indexed with SAMtools.

4. MultiQC

• aggregated results from Trim_Galore (Cutadapt,FastQC) and STAR alignments into one page.

5. Differential Expression

• this was edited and run in RStudio, outside of this snakemake automation workflow
• analysis script in bin/diffExp.Rmd
  • makes extensive use of vari-bbc/bbcRNA package wrapper functions for differential expression with edgeR.
  • some paths within this doc refer to local machine directory structure, will need modification to reproduce analysis (in particular, take note when importing STAR counts and STAR alignment metrics)
• the HTML report knitted from the .Rmd will contain the original code in collapsable boxes for reference.