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Old 12-01-2011, 10:54 AM   #1
Location: Seattle

Join Date: Jul 2011
Posts: 98
Default unmapped reads assigned to chromosomes

If I use samtools' "idxstats" commands, it returns information with:

1. reference sequence name (chromosome name in my case)

2. length of reference sequence

3. number of mapped reads assigned to that reference sequence

4. number of unmapped reads assigned to that reference sequence

Number 4 makes no sense to me. If a read is unmapped then by definition you can't assign it to a genomic location. If I remove everything with map quality less than 1, most of these go away but not all of them, i.e. I still end up with unmapped reads assigned to chromosomes. Does anyone understand this?

Thank you.

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