SEQanswers

Go Back   SEQanswers > Applications Forums > Genomic Resequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
how to determine the RPM threshold for MeDIP zchou Bioinformatics 0 12-01-2011 02:52 AM
Determine paired end overlapping chariko Bioinformatics 2 04-29-2011 12:52 AM
You Determine the Next Innovative Technology kevotu General 3 11-02-2010 09:00 AM
How to determine the insert length? anyone1985 Bioinformatics 7 08-16-2010 05:00 PM
how to determine the fist position of a genome biocc General 1 08-02-2010 08:02 AM

Reply
 
Thread Tools
Old 08-09-2010, 10:36 AM   #1
biocc
Member
 
Location: beijing

Join Date: Jul 2008
Posts: 35
Default how to determine a snp ?

hi, i resequenced a mutated bacteria genome, and want to detect the mutation information. at a position, i found half of the reads mapped are different from the reference, and half are the same . so some software reported it as snp, and some not. how to determine it as a SNP. how did this happened.
thanks.
biocc is offline   Reply With Quote
Old 08-10-2010, 03:41 AM   #2
svl
Member
 
Location: Netherlands

Join Date: Sep 2009
Posts: 43
Default

It could be a heterozygous SNP. Also errors can/will always occur (in sequencing, mapping), you might want to look at quality values as well.
svl is offline   Reply With Quote
Old 11-26-2010, 09:58 AM   #3
ntremblay
Member
 
Location: Montreal, Quebec, Canada

Join Date: Dec 2009
Posts: 27
Default

Hi,

if you encounter an interesting SNP in your analysis, the quickest way to determine if it's real or not would be to confirm it with an independant method like PCR + Sanger ...
ntremblay is offline   Reply With Quote
Old 11-26-2010, 07:48 PM   #4
drio
Senior Member
 
Location: 4117'49"N / 24'42"E

Join Date: Oct 2008
Posts: 323
Default

If you have a very small number of SNPs, validate them by eye. Display the alignments at the SNP position and see if the call makes sense. Ultimately of course validate via sanger.
__________________
-drd
drio is offline   Reply With Quote
Old 11-26-2010, 08:47 PM   #5
biocc
Member
 
Location: beijing

Join Date: Jul 2008
Posts: 35
Default thanks

Quote:
Originally Posted by drio View Post
If you have a very small number of SNPs, validate them by eye. Display the alignments at the SNP position and see if the call makes sense. Ultimately of course validate via sanger.
yes, i did it by eye through Tablet. i found some reads aligned are A and some aligned are G. if all these reads are unique, how should i determinate? thaks
biocc is offline   Reply With Quote
Old 11-27-2010, 02:51 PM   #6
drio
Senior Member
 
Location: 4117'49"N / 24'42"E

Join Date: Oct 2008
Posts: 323
Default

Post here a screenshot of the alignments (tablet) for one of the snps and then we can discuss. The original SAM alignments for the SNP would help also.
__________________
-drd
drio 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 07:26 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO