SEQanswers

Go Back   SEQanswers > Applications Forums > De novo discovery



Similar Threads
Thread Thread Starter Forum Replies Last Post
Coverage "standards" for SNP detection in tumor samples giorgifm Bioinformatics 7 06-26-2013 03:41 PM
Coverage required for SNP detection? Kasycas De novo discovery 3 04-12-2011 11:38 PM
coverage and SNP detection rudi283 Bioinformatics 0 03-29-2011 08:22 AM
PubMed: Pyrosequencing-based strategy for a successful SNP detection in two hypervari Newsbot! Literature Watch 0 01-20-2010 03:10 AM
Number of runs required SNP detection transcriptome Tombre Illumina/Solexa 1 08-20-2009 11:13 AM

Reply
 
Thread Tools
Old 08-12-2011, 05:22 AM   #1
gavin.oliver
Senior Member
 
Location: uk

Join Date: Jan 2010
Posts: 110
Default Coverage required for Sanger based SNP detection and Genotyping

Does anyone know of an established acceptable figure in terms of times coverage required for SNP/calling and genotyping with Sanger sequences?

I know 20x is generally recommended for NGS but this is obviously a different scenario.
gavin.oliver is offline   Reply With Quote
Old 08-30-2011, 12:54 AM   #2
sciencewu
Member
 
Location: china

Join Date: Dec 2010
Posts: 12
Default

many papers using the Sanger sequences ,but didn't give a criteria . maybe 10x is enough.
sciencewu is offline   Reply With Quote
Old 08-30-2011, 01:33 AM   #3
prm36
Member
 
Location: Edinburgh

Join Date: Mar 2010
Posts: 16
Default

We take 2x coverage for SNP calling in our lab.

Ventner's genome was done to 7.5x (http://www.nature.com/nrg/journal/v1...df/nrg2626.pdf)

Cheers

Paul
prm36 is offline   Reply With Quote
Old 08-30-2011, 01:41 AM   #4
sciencewu
Member
 
Location: china

Join Date: Dec 2010
Posts: 12
Default

Did you get a good result ? what's FP and FN ?
sciencewu is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 05:43 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO