SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Illumina vs. Agilent Exome enrichment - higher false positive rates markusl Genomic Resequencing 9 09-22-2016 07:22 AM
samtools false positive/negative dnusol Bioinformatics 0 11-08-2011 07:13 AM
tophatfusion false positive results lichenbiostat RNA Sequencing 0 10-30-2011 09:37 AM
SNPs false positive GATK jtrivino Bioinformatics 0 05-06-2011 03:28 AM
False Discovery Rate issue slny Bioinformatics 1 04-05-2011 02:35 AM

Reply
 
Thread Tools
Old 06-20-2010, 08:06 AM   #1
yi2004
Junior Member
 
Location: Singapore

Join Date: Jun 2010
Posts: 3
Default ti/tv ratio and false positive SNP rate

I learned that estimated false positive SNP rate=1- (observed_ti/tv_ratio-0.5)/(expected_ti/tv_ratio-0.5). In one of our re-sequencing data, the observed ti/tv ratio for coding region is 3.0 (while expected ti/tv ratio for exome is 2.8). But false positive rate can not be negative...
yi2004 is offline   Reply With Quote
Old 06-20-2010, 09:43 AM   #2
Pepe
Member
 
Location: Germany

Join Date: Mar 2009
Posts: 28
Default

What do ti and tv stand for?
Pepe is offline   Reply With Quote
Old 06-20-2010, 11:35 AM   #3
nilshomer
Nils Homer
 
nilshomer's Avatar
 
Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285
Default

Quote:
Originally Posted by Pepe View Post
What do ti and tv stand for?
Transition and transversion mutation rates.
nilshomer is offline   Reply With Quote
Old 06-20-2010, 06:37 PM   #4
yi2004
Junior Member
 
Location: Singapore

Join Date: Jun 2010
Posts: 3
Default

Does anybody know why the false positive SNP rate is estimated as
1- (observed_ti/tv_ratio-0.5)/(expected_ti/tv_ratio -0.5)?
Any reference to this is much appreciated.
yi2004 is offline   Reply With Quote
Old 06-20-2010, 07:23 PM   #5
nilshomer
Nils Homer
 
nilshomer's Avatar
 
Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285
Default

Quote:
Originally Posted by yi2004 View Post
Does anybody know why the false positive SNP rate is estimated as
1- (observed_ti/tv_ratio-0.5)/(expected_ti/tv_ratio -0.5)?
Any reference to this is much appreciated.
I used google:
http://www.megasoftware.net/WebHelp/...on_ratio_r.htm
nilshomer is offline   Reply With Quote
Old 06-21-2010, 02:07 AM   #6
yi2004
Junior Member
 
Location: Singapore

Join Date: Jun 2010
Posts: 3
Smile

Quote:
Originally Posted by nilshomer View Post
Thanks Nilshomer! I will have a look at the website you pointed at, and hope I can figure out the answer to my question...
yi2004 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 05:50 PM.


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