Overview

FireCloud Method: xavier-genomics/bulk_rna_seq

The RNA-Seq pipelines takes raw reads (in fastq format) and outputs QC metrics, a gene counts matrix, and differential expression between specified conditions. Currently, it accepts data only from paired-end experiments, but we are working to include 3’/5’ DGE as well. The steps (broadly) are as follows:

1. Create a kallisto index for the specified reference transcriptome (if this has not already been done)
2. Perform pre-alignment QC on each sample
3. Pseudoalign reads to reference transcriptome, generate transcript counts, and get alignment QC metrics (via kallisto)

4. Map from transcript counts to gene counts, output gene counts (if user wants to run differential expression via edgeR on their own), and perform differential expression (via sleuth)

5. Combine pre-alignment and alignment QC via multiQC