This tool is the equivalent of fq2bam for RNA-Seq samples, receiving inputs in FASTQ format, performing alignment with the splice-aware STAR algorithm, optionally marking of duplicate reads, and outputting an aligned BAM file ready for variant and fusion calling.

For further information visit the [rna-fq2bam help page](https://docs.nvidia.com/clara/parabricks/4.0.0/Documentation/ToolDocs/man_rna_fq2bam.html#man-rna-fq2bam).

## Quick Start

    # This command assumes all the inputs are in <INPUT_DIR> and all the outputs go to <OUTPUT_DIR>.
    $ docker run --rm --gpus all --volume <INPUT_DIR>:/workdir --volume <OUTPUT_DIR>:/outputdir
        -w /workdir \
        nvcr.io/nvidia/clara/clara-parabricks:<VERSION-TAG> \
        pbrun rna_fq2bam \
        --in-fq /workdir/${INPUT_FASTQ_1} /workdir/${INPUT_FASTQ_2} \
        --genome-lib-dir /workdir/${PATH_TO_GENOME_LIBRARY}/ \
        --output-dir /outputdir/${PATH_TO_OUTPUT_DIRECTORY} \
        --ref /workdir/${REFERENCE_FILE} \
        --out-bam /outputdir/${OUTPUT_BAM} \
        --read-files-command zcat

clara-parabricks-rna-fq2bam

Run RNA-seq data through the fq2bam pipeline. It will run STAR aligner, co-ordinate sorting and mark duplicates.

Nvidia Clara Parabricks rna-fq2bam

Quick Start