Question: Existing Tools For Post-Processing After Aligning Paired-End Reads With Blat?
0
gravatar for Tianyang Li
5.1 years ago by
Tianyang Li460
Beijing, China
Tianyang Li460 wrote:

Hi,

I'm wondering if there are existing tools that can do post-processing on paired-end reads' BLAT output.

More specifically, I'd like the tool to "merge" the alignments from the alignments of each pair's ends and remove the inconsistent alignments while keeping the consistent ones. The tool should also produce output in PSL, SAM, or BAM.

Thanks!

paired-end blat • 1.5k views
ADD COMMENTlink written 5.1 years ago by Tianyang Li460
1
gravatar for Damian Kao
5.1 years ago by
Damian Kao14k
UK
Damian Kao14k wrote:

If you convert your blat output into a .bed file, you can used bedtools (http://code.google.com/p/bedtools/) to merge the features.

ADD COMMENTlink written 5.1 years ago by Damian Kao14k
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