Skip to main content

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


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

rnasa-0.2.0.tar.gz (11.6 kB view hashes)

Uploaded Source

Built Distribution

rnasa-0.2.0-py3-none-any.whl (12.9 kB view hashes)

Uploaded Python 3

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page