Metadata-Version: 2.1
Name: rnasa
Version: 0.1.2
Summary: Gene Expression Level Calculator for RNA-seq
Home-page: https://github.com/dceoy/rnasa
Author: Daichi Narushima
Author-email: dnarsil+github@gmail.com
License: UNKNOWN
Description: rnasa
        =====
        
        Gene Expression Level Calculator for RNA-seq
        
        ![Test](https://github.com/dceoy/rnasa/workflows/Test/badge.svg)
        ![Upload Python Package](https://github.com/dceoy/rnasa/workflows/Upload%20Python%20Package/badge.svg)
        
        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
        -----
        
        1.  Download and process resource data.
        
            ```sh
            $ rnasa download --genome=GRCh38 --dest-dir=/path/to/ref
            ```
        
        2.  Calculate TPM (transcripts per million) values.
        
            ```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.
        
        3.  Extract TPM values from RSEM results files.
        
            ```sh
            $ rnasa extract --dest-dir=. /path/to/output/rsem
            ```
        
        Run `rnasa --help` for more information.
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: MacOS
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.6
Description-Content-Type: text/markdown
