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Forum: Bioinformatics 04-28-2014, 11:58 AM
Replies: 1
Views: 2,433
Posted By persorrels
Filter somatic calls in Pindel output

I'm running Pindel on some normal/tumor pairs. A lot of calls seem to be germline. Is there a filtering script out there to get the somatic calls?
Forum: Bioinformatics 02-14-2014, 09:31 AM
Replies: 0
Views: 1,301
Posted By persorrels
How does BWA MEM handle reads shorter than 70bp?

Yet another quality trimming question... I've got some Illumina paired-end DNAseq data from tumor and normal samples (100bp reads). I want to align the data using BWA mem, but I'm worried that some...
Forum: Bioinformatics 10-04-2013, 11:16 AM
Replies: 6
Views: 5,462
Posted By persorrels
Human, 10x exome. Total sequence size is about...

Human, 10x exome. Total sequence size is about 30Gb. 100bp per read. Attached are some sample statistics from reverse reads.
Forum: Bioinformatics 10-04-2013, 09:28 AM
Replies: 1
Views: 2,816
Posted By persorrels
Did you get a new insight on this problem? I...

Did you get a new insight on this problem? I posted a similar question here:

http://seqanswers.com/forums/showthread.php?p=117919#post117919
Forum: Bioinformatics 10-04-2013, 09:22 AM
Replies: 6
Views: 5,462
Posted By persorrels
Vishnu, thanks for your reply. It is true...

Vishnu, thanks for your reply.

It is true that most forward reads are of high quality. But the reverse reads aren't. Below are two examples:


...
Forum: Bioinformatics 10-03-2013, 09:54 AM
Replies: 6
Views: 5,462
Posted By persorrels
Minimum Read Length for BWA

Hi all,

I am preprocessing a dataset from a human sample sequenced by Illumina HiSeq 2500 (Paired-end reads, 100bp each). I first trim each read based on quality. If the trimmed sequence is too...
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