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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?

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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.

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

Seen: 156 times

Last updated: Apr 03 '13