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  • Unmapping reads in bam file

    Hi,

    I need to mark reads mapped to a particular chromosome as unmapped in aligned bam file. The fastq files were aligned using an fasta file with one more chromosome than is present in our standard assembly. If possible I would like to avoid converting everything back to fastq and starting all over.

    In particular, what needs to be done apart from setting the third bit in FLAGS? I notice that my bam files have reads with the third bit set, but which also have chromosome positions when I "samtools view" the bam file.

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