SRR6269612 170103_SN898_0752_BCA0WJACXX_2_ID08 ICD_IND-PPCTC.PPTC-TGT-258-R-1_1pA-23 1 NIL StarRNAseqAligner 2.3.0e {StarRNAseqAligner} --genomeDir {reference} --readFilesCommand zcat --readFilesIn {FASTQfile1} {FASTQfile2} --runThreadN 8 --outFilterMultimapNmax 20 --outFilterMismatchNoverLmax 0.04 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignIntronMax 200000 --outSAMstrandField intronMotif --outStd SAM --outSAMunmapped Within | {samtools} view - -b -S -o {outputDir}/BAM/{eventId}.temp.bam 2 1 picard 1.54 {java} -Xmx22G -jar {picard_1_54_dir}/AddOrReplaceReadGroups.jar INPUT={outputDir}/BAM/{eventId}.temp.bam OUTPUT={outputDir}/BAM/{eventId}_sorted.bam SORT_ORDER=coordinate RGID="{eventId}" RGLB="{libraryName}" RGPL="Illumina" RGSM="{eventId}" RGCN="BCM" RGPU="{platformUnit}" TMP_DIR=/space1/tmp MAX_RECORDS_IN_RAM=3000000 VALIDATION_STRINGENCY=SILENT 3 2 picard 1.54 {java} -Xmx4g -jar {picard_1_54_dir}/ReorderSam.jar I={outputDir}/BAM/{eventId}_sorted.bam O={outputDir}/BAM/{eventId}_duplicates.bam REFERENCE={reference}/reference.fa TMP_DIR=/space1/tmp MAX_RECORDS_IN_RAM=3000000 VALIDATION_STRINGENCY=SILENT 4 3 picard 1.54 {java} -Xmx4g -jar {picard_1_54_dir}/MarkDuplicates.jar I={outputDir}/BAM/{eventId}_duplicates.bam O={outputDir}/BAM/{eventId}.bam AS=true M={outputDir}/Stats/{eventId}_metrics.txt TMP_DIR=/space1/tmp MAX_RECORDS_IN_RAM=3000000 VALIDATION_STRINGENCY=SILENT 5 4 samtools 0.1.19 {samtools} index {outputDir}/BAM/{eventId}.bam 6 5 RNA-SeQC 1.1.7 {java} -Xmx5g -jar {rnaseqQC} -BWArRNA {rRNA} -bwa {oldbwa} -s {outputDir}/RNA-SeQC/event_file.txt -t {reference}/reference.gtf -r {reference}/reference.fa -o {outputDir}/RNA-SeQC 7 6 cufflinks 2.1.1 {cufflinks} -G {reference}/reference.gtf {outputDir}/BAM/{eventId}.bam -q -o {outputDir}/Cufflinks -p 4 --no-update-check 8 7 ERCCPlot 1.0 {java} -Xmx1g -jar {ERCCPlot} -c {outputDir}/Cufflinks/genes.fpkm_tracking -e {ERCCConc} -o {outputDir}/ERCC-QC 9 8 ERCCStats 1.0 {ERCCStats} {outputDir}/BAM/{eventId}.bam > {outputDir}/ERCC-QC/erccStats.txt