SEQanswers

Go Back   SEQanswers > General



Similar Threads
Thread Thread Starter Forum Replies Last Post
tophat in background sbrohee Bioinformatics 1 10-12-2011 06:39 AM
BWA in the background ercfrtz Bioinformatics 7 04-21-2011 08:04 AM
PubMed: Enhanced mismatch mutation analysis: simultaneous detection of point mutation Newsbot! Literature Watch 0 12-14-2010 02:20 AM
mutation or mismatch rate per base foxytomato Bioinformatics 0 07-01-2010 07:56 AM
newbler background Tom Bair 454 Pyrosequencing 11 10-26-2009 12:12 AM

Reply
 
Thread Tools
Old 03-07-2012, 06:28 PM   #1
dimo
Member
 
Location: Australia

Join Date: Mar 2012
Posts: 10
Default Background mutation rate

Greetings and salutations,

I have somewhat simple question which I can not seem to get a consensus on based on literature. Long story short I have a whole bunch of whole exome sequencing data for cancer samples. I want to identify potential genes of interest in these samples, to do so I need a background mutation rate. My question is how does one calculate a simple background mutation rate (for now disregard differences in mutation rates between transversions, transitions, CpG islands etc). Is it simply the number of synonymous mutations / bp sequenced? Or does the number of non-synonymous mutations as well as location of synonymous mutations also come into calculating background mutation rate. Or am I way off?

Thank you in advance

-Dmitri

Last edited by dimo; 03-07-2012 at 07:02 PM.
dimo is offline   Reply With Quote
Old 04-16-2012, 01:24 PM   #2
bioinfosm
Senior Member
 
Location: USA

Join Date: Jan 2008
Posts: 482
Default

I just posted this on biostar

http://www.biostars.org/post/show/17...vegicus/#42809

This paper (http://www.sciencemag.org/content/314/5797/268), especially the supplement (http://www.sciencemag.org/content/31.../268/suppl/DC1) talks about calculating it.
__________________
--
bioinfosm
bioinfosm 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 03:18 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO