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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
samtools sort -n myinput.bam myinput.sortByName.bam
samtools sort -n myinput.bam myinput.sortByName
Using sorted bam file to extract paired end fastq files
Using sorted bam file to extract paired end fastq files
