rnasa
Gene Expression Level Calculator for RNA-seq
Installation
$ pip install -U rnasa
Dependent commands:
pigzpbzip2bgzipsamtools(andplot-bamstats)javafastqctrim_galoreSTARrsem-prepare-referencersem-refseq-extract-primary-assemblyrsem-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
STARrsem-calculate-expression
- Collect QC metrics
fastqcsamtools
- Trim adapters
-
Extract TPM values from RSEM results files, and consolidate them into TSV files.
$ rnasa extract --dest-dir=. /path/to/output/rsem
If
--gctis passed,rnasa extractcreates output files in GCT format.
Run rnasa --help for more information.
1 maintainer
Metadata
1 maintainer
Release files for rnasa 0.2.0
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| File | Size | Uploaded | Provenance | Actions |
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| rnasa-0.2.0-py3-none-any.whl | Python 3 | none | any | Details for rnasa-0.2.0-py3-none-any.whl |
Total release size: 24.4 kB
Release files / rnasa-0.2.0.tar.gz
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| Size | 11.6 kB |
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| Tags | Python 3 |
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