| Name | rnasa JSON |
| Version |
0.2.0
JSON |
| download |
| home_page | https://github.com/dceoy/rnasa |
| Summary | Gene Expression Level Calculator for RNA-seq |
| upload_time | 2023-12-23 06:31:51 |
| maintainer | |
| docs_url | None |
| author | Daichi Narushima |
| requires_python | >=3.6 |
| license | |
| keywords |
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
rnasa
=====
Gene Expression Level Calculator for RNA-seq
[](https://github.com/dceoy/rnasa/actions/workflows/test.yml)
[](https://github.com/dceoy/rnasa/actions/workflows/python-publish.yml)
[](https://github.com/dceoy/rnasa/actions/workflows/docker-publish.yml)
Installation
------------
```sh
$ 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](https://hub.docker.com/r/dceoy/rnasa/).
```sh
$ 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.
```sh
$ rnasa download --genome=GRCh38 --dest-dir=/path/to/ref
```
2. Calculate TPM (transcripts per million) values from FASTQ files.
```sh
$ 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.
```sh
$ 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.
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