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Gene Expression Level Calculator for RNA-seq

Project description

rnasa

Gene Expression Level Calculator for RNA-seq

Test Upload Python Package CI to Docker Hub

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

input files output files
FASTQ (Illumina) TSV (or GCT)
  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.

Project details


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