Bowtie / Feature Requests / #54 Request strand info in Crossbow output

Request strand info in Crossbow output

#54 Request strand info in Crossbow output

Status: open

Owner: nobody

Labels: None

Priority: 5

Updated: 2010-09-19

Created: 2010-09-19

Creator: Anonymous

Private: No

Crossbow's minor adaptation of the SoapSNP output format has lots of useful info, but it's apparently missing a piece key to further annotation: strand. Tools like EBI's SNP Effect Predictor http://uswest.ensembl.org/info/website/upload/index.html#Consequence want it -- obviously, the effect on protein coding is different; upstream/downstream distance criteria, etc. You have this information internally, because Bowtie produces it. So how about adding another column?

Cheers!
Howie Goodell

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Anonymous - 2010-09-27

Hi --

Please cancel this request; my misunderstanding. I realize strand info for follow-on packages should always be "+"; since you convert position and complement bases where you align reads from the reverse strand.

Thanks!
Howie Goodell

Hi -- Please cancel this request; my misunderstanding. I realize strand info for follow-on packages should always be "+"; since you convert position and complement bases where you align reads from the reverse strand. Thanks\! Howie Goodell

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#54 Request strand info in Crossbow output

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