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, 16:17, 18 March 2010
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| In order to extract paired end reads, the BAM file has to be sorted by name, e.g. using samtools. Suppose the BAM file is myinput.bam | | In order to extract paired end reads, the BAM file has to be sorted by name, e.g. using samtools. Suppose the BAM file is myinput.bam |
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− | samtools sort -n myinput.bam myinout.sortByName.bam | + | samtools sort -n myinput.bam myinput.sortByName.bam |
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| Using sorted bam file to extract paired end fastq files | | Using sorted bam file to extract paired end fastq files |