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--first firstReadInAPair_FastQ
--first firstReadInAPair_FastQ
--second secondReadInAPair_FastQ
--second secondReadInAPair_FastQ
--single unpairedReads_FastQ
--unpaired unpairedReads_FastQ
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
