Bowtie / Feature Requests / #42 unqiue mapping

unqiue mapping

#42 unqiue mapping

Status: pending

Owner: Ben Langmead

Labels: bowtie (72)

Priority: 5

Updated: 2015-12-07

Created: 2010-02-20

Creator: Anonymous

Private: No

hi there,
i want to only get the reads mapped to genome uniquely. the last item in bowtie's result indicates how many other loci where the read can be mapped on the SAME strand. it is still 0 when it can be mapped to other loci on the other strand. i am not sure if there other ways i can get these information.

jing

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Ben Langmead - 2011-12-21

I am not sure what output you are referring to. Can you reply with more details?

Ben

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Ben Langmead - 2011-12-21

status: open --> pending
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Robert Literman - 2015-12-07

I second this request. It would be VERY helpful to have an output option for reads that map once and only once. Currently, you have to parse the BAM to get this, but since the output of Bowtie2 already tells you how many reads map exactly once, it seems like that data is already in there somewhere and could be pumped out with a --unique flag or something?

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unqiue mapping

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#42 unqiue mapping

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