Daucus_syrticus_Ames_29108

Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' >name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam >name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1本BAM格式文件（Binary Alignment Map）包含所有比对至单个质体参考序列的测序读段。该参考序列仅包含1个反向重复序列（inverted repeat）。 用于生成该BAM文件的命令如下： bwa mem -a -M -t 8 -R "@RG ID:Accession LB:barcode PL:illumina SM:accession_number PI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' >name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam >name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam 所用软件版本信息如下： bwa版本：0.7.15-r1140 samtools版本：0.1.19-44428cd Java版本：1.8.0_111 Picard版本：2.7.1