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  • Given a merged BAM file, how do I convert it to 2 PE reads and 1 SE read?

    I have a couple of .bam files, each one consists of merging 1 paired end .bam and 1 single end .bam file.

    How do I extract essentially the 3 .fastq files from each .bam file?

    I was thinking about using bedtools bamtofastq, but it doesn't have the option that I am looking for.

  • #2
    Actually, I forgot one important detail, the .bam file with PE reads mapped might have been mapped using an interleaved .fastq file, so I would be expecting to get 2 .fastq files, 1 for PE interleaved read file and 1 for SE read file.

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