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Thread | Thread Starter | Forum | Replies | Last Post |
Sort of a noob here: looking for somatic mutation in tumors (NGS sequencing) | lethalfang | Bioinformatics | 8 | 10-07-2013 12:08 AM |
NGS software for somatic de novo mutation | carolW | Bioinformatics | 1 | 05-27-2013 01:42 AM |
Identifying Somatic mutation candidates question | Phantom123 | Bioinformatics | 0 | 03-26-2012 07:47 AM |
Paired-sample (tumor/normal) somatic mutation detection software | alexischr | Bioinformatics | 1 | 04-14-2011 05:56 AM |
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#1 |
Junior Member
Location: Taiwan Join Date: Jun 2013
Posts: 3
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Dear all
I have a project to analysis somatic mutation from clinical sample, maybe serum. I will choose some gene and design PCR primer to amplify target exon region. These amplicon will sequenced over 500X by using Illuminar Miseq 150PE. My question is, how to analysis or define "somatic mutation". Because the sequence depth is really high, I think the sequence data will has some sequence error to interfere somatic mutation calling, how can I filter out this possible bias? Reads trimming using QV 30 instead of QV20? Thanks for any help, WT |
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#2 |
Senior Member
Location: Hong Kong Join Date: Mar 2010
Posts: 498
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I think the standard approach is that you also sequence germline DNA. Then you can use it to filter out the germline mutations from the mutations you find. The remaining ones should be somatic mutations
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