SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
[BMC] Single-nucleotide resolution analysis of the transcriptome structure of Clos. sdwy2008 Literature Watch 0 10-06-2011 02:53 PM
PubMed: galign: a tool for rapid genome polymorphism discovery. Newsbot! Literature Watch 0 09-26-2009 03:04 AM
PubMed: Transcriptome content and dynamics at single-nucleotide resolution. Newsbot! Literature Watch 0 10-03-2008 06:00 AM

Reply
 
Thread Tools
Old 07-09-2010, 12:40 AM   #1
ramouz87
Member
 
Location: Doha, Qatar

Join Date: Oct 2009
Posts: 35
Default Single nucleotide polymorphism (SNP) discovery in polyploid

Hi,
I would like to find SNP in polyploid organism(having more than 2 chromosomes), is there any SNP discovery tool that can handel that ?
If not, anyone know how to compute SNP confidence score from concensus call in this case ?
Thanks in adavnce for your suggestions
Best,
Ramzi
ramouz87 is offline   Reply With Quote
Old 07-09-2010, 08:25 AM   #2
nilshomer
Nils Homer
 
nilshomer's Avatar
 
Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285
Default

Quote:
Originally Posted by ramouz87 View Post
Hi,
I would like to find SNP in polyploid organism(having more than 2 chromosomes), is there any SNP discovery tool that can handel that ?
If not, anyone know how to compute SNP confidence score from concensus call in this case ?
Thanks in adavnce for your suggestions
Best,
Ramzi
Not too sure, but what about the "-N" option in "samtools pileup"? I say I am not too sure since I am not sure how SNPs with one out of N copies will be reported (N>2).
nilshomer 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 08:32 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO