rnasa

Gene Expression Level Calculator for RNA-seq

Installation

$ pip install -U rnasa

Dependent commands:

Pull the image from Docker Hub.

$ docker image pull dceoy/rnasa

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:
1. Trim adapters
  - trim_galore
2. Map reads and calculate TPM values
  - STAR
  - rsem-calculate-expression
3. 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.

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution for rnasa 0.2.0
File	Size	Uploaded
rnasa-0.2.0.tar.gz	11.6 kB	Dec 23, 2023	Details

Table of built distributions (wheels) for rnasa 0.2.0
File	Interpreter	ABI	Platform	Reset
rnasa-0.2.0-py3-none-any.whl 12.9 kB Dec 23, 2023	Python 3	none	any	Details

Total release size: 24.4 kB

Download URL	rnasa-0.2.0.tar.gz
Size	11.6 kB
Tags	Source
SHA-256 checksum How to use checksums	`178b35aa55195180d675b8a53f00fdf11eb315b01566baac475f951e8ffe90c3`
BLAKE2b-256 checksum How to use checksums	`d6dbd62301110d4024b7b33c869269d56fcfb47ae51c113a6165c04f7956851f`
Upload date	Dec 23, 2023
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.9.18`

Download URL	rnasa-0.2.0-py3-none-any.whl
Size	12.9 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`2dd92326809eaba8f304e988828deea853a8fa604ba0d5f539fcca4a4d08ec0b`
BLAKE2b-256 checksum How to use checksums	`614e2c08d8a71c7b0928faa94add63042e5f4bf000003904fb977389500366d3`
Upload date	Dec 23, 2023
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.9.18`