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Old 07-20-2012, 05:01 AM   #1
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Location: Europe

Join Date: Dec 2011
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Question Unmapping reads in bam file


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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bam unmap format

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