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Generating unaligned reads from aligned data gives you the flexibility to remap the reads using either a different aligner, a different set of alignment parameters, or a different genome reference. This is particularly useful in analyzing sequences from xenograft models where the same set of reads can be aligned two two different species. It may also be useful if the original unaligned FASTQ files are not as easily accessible to the user as the aligned BAM files.

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During the conversion, the BAM files are converted to FASTQ files.  If the BAM file contains paired end reads, two FASTQ files will be generated for each BAM, and the files names will contain _1 and _2. An example  in figure Figure 3 shows 18 fastq.gz files from 9 .bam files.

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