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Daucus_crinitus_652412

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posted on 18.12.2019 by David M. Spooner, Holly Ruess, Massimo Iorizzo, Douglas Senalik, Philipp Simon
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

History

dc.format.extent

352451189

dc.identifier.uri

http://hdl.handle.net/10255/dryad.135923

dwc.ScientificName

Apiaceae, Daucus

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