expression

The expression module is responsible for determining gene expression levels from STAR bam and count files. Although the strandedness of the library preparation is important when determining, the module itself is strand agnostic. Instead, we take inspiration from STAR and produce output files for unstranded, forward stranded and reverse stranded libraries, and leave it to the user to select the relevant output for their samples.

Tools

This module relies on the STAR count files in combination with a set of housekeeping genes to normalize gene expression levels.

Input

The input for this module is one BAM file and one STAR count table specified in a PEP configuration file, as is shown below.

Example input for the expression module
sample_name	bam	count
SRR8615409	test/data/expression/SRR8615409.bam	test/data/expression/SRR8615409.ReadsPerGene.out.tab

Output

Three files with the normalized gene expression levels, one for each strandedness.
A single MultiQC report which contains the same data.

Configuration

The following options are available for the expression module

Example

{
  "housekeeping": [
    "MT-CO2"
  ],
  "gtf": "test/data/reference/hamlet-ref.gtf",
  "bed": "test/data/reference/transcripts_chrM.bed"
}

Configuration options

Configuration options
Option	Description	Required
housekeeping	A list of genes to use for normalizing the expression	yes
gtf	A GTF file, to look up the ENSG for the housekeeping genes	yes
bed	A BED file with genomic regions (genes) to quantify	yes