Question: Is there a tool to convert soft clipping to hard clipping in bam files?
0
gravatar for Ryan Thompson
18 months ago by
Ryan Thompson3.3k
TSRI, La Jolla, CA
Ryan Thompson3.3k wrote:

My lab is developing a pipeline to analyze some paired-end methyl-seq data. One of the steps is to soft-clip overlaps between read pairs to prevent downstream tools from double-counting the overlapped region, using bamutil clipOverlap (http://genome.sph.umich.edu/wiki/BamUtil:_clipOverlap). However, one of the downstream tools, methylKit, will not accept soft-clipped reads, so I would like to convert the soft clipping to hard clipping in order to input it into methylKit. Is there a tool for converting soft clipping into hard clipping? Or is the conversion simple enough to implement myself?

bam clipping • 698 views
ADD COMMENTlink modified 18 months ago • written 18 months ago by Ryan Thompson3.3k
2

FYI, PileOMeth has a --methylKit option that will create methlyKit-compatible output and not require you to do any mucking around with artificially hard/soft clipping bases. Perhaps that already does what you need.

ADD REPLYlink written 18 months ago by Devon Ryan73k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1339 users visited in the last hour