Daucus_setulosus_652360
收藏DataONE2017-03-10 更新2024-06-26 收录
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资源简介：
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（Binary Alignment Map）文件包含所有比对至单个质体参考序列的测序读段（reads）。该参考序列仅包含1个反向重复序列。
创建该BAM文件所使用的命令如下：
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
所用工具版本信息如下：
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
创建时间：
2017-03-10
