Ask Your Question

Is there a way to view bases that have been softclipped from reads?

asked 2013-04-03 11:32:51 -0600

Lee Baker gravatar image

I would like to view bases that have been softclipped from reads in the pileup. Ideally, they should be shaded a different color or otherwise visually distinguished from normal bases.

Currently I'm using IGV to do this - is there a way to enable this in GenomeBrowse?

edit retag flag offensive close merge delete

1 answer

Sort by ยป oldest newest most voted

answered 2013-04-03 15:14:15 -0600

MichaelThiesen gravatar image

Currently there isn't any way to see soft-clipped bases in the pile-up. The only way to see soft-clipped bases is to click on an alignment and look at the raw sequence in the data console.

We may add an option to draw soft-clipped bases in future versions of GenomeBrowse though, so keep an eye open for updates.

edit flag offensive delete link more
Login/Signup to Answer

Questions should be tagged FeatureRequest for asking about a non-existing feature or proposing a new idea, GeneralInquiry for general questions about GenomeBrowse or directions on how to do something, or RanIntoProblem if you want to report an issue or had difficulty getting to an expected result.


Asked: 2013-04-03 11:32:51 -0600

Seen: 539 times

Last updated: Apr 03 '13