rna_fq2bam

            

            
# This command assumes all the inputs are in the current working directory and all the outputs go to the same place.
docker run --rm --gpus all --volume $(pwd):/workdir --volume $(pwd):/outputdir \
    --workdir /workdir \
    nvcr.io/nvidia/clara/clara-parabricks:4.5.1-1 \
    pbrun rna_fq2bam \
    --in-fq /workdir/${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
        

            

            
# STAR Alignment
$ ./STAR \
      --genomeDir <INPUT_DIR>/${PATH_TO_GENOME_LIBRARY} \
      --readFilesIn <INPUT_DIR>/${INPUT_FASTQ_1} <INPUT_DIR>/${INPUT_FASTQ_2} \
      --outFileNamePrefix <OUTPUT_DIR>/${PATH_TO_OUTPUT_DIRECTORY}/ \
      --outSAMtype BAM SortedByCoordinate \
      --readFilesCommand zcat

# Mark Duplicates
$ gatk MarkDuplicates \
    --java-options -Xmx30g \
    -I Aligned.sortedByCoord.out.bam \# This filename is determined by STAR.
    -O <OUTPUT_DIR>/${NAME_OF_OUTPUT_BAM_FILE} \
    -M metrics.txt
        

            

            
# Add this line in ReadAlign::quantTranscriptome() function in ReadAlign_quantTranscriptome.cpp
rngMultOrder.seed(777);
# Add it right before:
alignT[int(rngUniformReal0to1(rngMultOrder)*nAlignT)].primaryFlag=true;