SRR3124371 140824_SN7001353_0385_BC4JYDACXX_7_ID01 ICD_IND-PEDCAR.T368R-1_1pA-6 1 NIL STAR STAR_2.3.1l_r335 star --genomeDir --readFilesIn 1.fastq 2.fastq --readFilesCommand "bzcat" --runThreadN 8 --outFilterMultimapNmax 20 --outFilterMismatchNoverLmax 0.04 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignIntronMax 200000 --outSAMstrandField intronMotif --outStd SAM --outSAMunmapped Within | samtools view - -b -S -o output.bam 2 1 Picard AddOrReplaceReadGroups 1.54 java -Xmx22G -jar Picard/AddOrReplaceReadGroups.jar INPUT=output.bam OUTPUT=output_sorted.bam SORT_ORDER=coordinate RGID=sample RGLB=library RGPL=Illumina RGSM=sample RGCN=BCM RGPU=puid TMP_DIR=/space1/tmp MAX_RECORDS_IN_RAM=3000000 VALIDATION_STRINGENCY=SILENT 3 2 Picard ReorderSam 1.54 java -Xmx4g -jar Picard/ReorderSam.jar I=output_sorted.bam O=output_duplicates.bam REFERENCE=reference.fasta TMP_DIR=/space1/tmp MAX_RECORDS_IN_RAM=3000000 VALIDATION_STRINGENCY=SILENT 4 3 Picard MarkDuplicates 1.54 java -Xmx4g -jar Picard/MarkDuplicates.jar I=output_duplicates.bam O=barcode.bam AS=true M=barcode_metrics.txt TMP_DIR=/space1/tmp MAX_RECORDS_IN_RAM=3000000 VALIDATION_STRINGENCY=SILENT 5 4 samtools index 0.1.11 samtools index barcode.bam assembly GRCh37