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bam2FastQ -i myinput.sortByName.BAM --first myread1.fastQ --second myread2.fastQ
bam2FastQ -i myinput.sortByName.BAM --first myread1.fastQ --second myread2.fastQ
Or to extract both paired end and single end fastq files
Or to extract both paired end and single end fastq files (if the bam file contains both single and paired end reads)
bam2FastQ -i myinput.sortByName.BAM --first myread1.fastQ --second myread2.fastQ --single myreadSingle.fastQ
bam2FastQ -i myinput.sortByName.BAM --first myread1.fastQ --second myread2.fastQ --single myreadSingle.fastQ
