rnasa

Gene Expression Level Calculator for RNA-seq

Installation

$ pip install -U rnasa

Dependent commands:

• pigz
• pbzip2
• bgzip
• samtools (and plot-bamstats)
• java
• fastqc
• trim_galore
• STAR
• rsem-prepare-reference
• rsem-refseq-extract-primary-assembly
• rsem-calculate-expression

Docker image

Pull the image from Docker Hub.

$ docker image pull dceoy/rnasa

Usage

Calculate gene expression levels

1. Download and process resource data.

   $ rnasa download --genome=GRCh38 --dest-dir=/path/to/ref

2. Calculate TPM (transcripts per million) values from FASTQ files.

   $ rnasa calculate \
       --workers=2 \
       --dest-dir=/path/to/output \
       /path/to/ref/GRCh38 \
       /path/to/sample1_fastq_prefix \
       /path/to/sample2_fastq_prefix \
       /path/to/sample3_fastq_prefix

   The command search for one (single-end) or two (paired-end) input FASTQ files by prefix.

   Standard workflow:

   1. Trim adapters
      • trim_galore
   2. Map reads and calculate TPM values
      • STAR
      • rsem-calculate-expression
   3. Collect QC metrics
      • fastqc
      • samtools

3. Extract TPM values from RSEM results files, and consolidate them into TSV files.

   $ rnasa extract --dest-dir=. /path/to/output/rsem

   If --gct is passed, rnasa extract creates output files in GCT format.

Run rnasa --help for more information.