Description:

rnasa 0.2.0

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



input files
output files




FASTQ (Illumina)
TSV (or GCT)





Download and process resource data.
$ rnasa download --genome=GRCh38 --dest-dir=/path/to/ref



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:

Trim adapters

trim_galore


Map reads and calculate TPM values

STAR
rsem-calculate-expression


Collect QC metrics

fastqc
samtools





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.

License

For personal and professional use. You cannot resell or redistribute these repositories in their original state.

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