SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
How To: Contig to Scaffold? fahmida Bioinformatics 3 08-22-2013 04:41 AM
scaffold and contig chengeng Bioinformatics 5 07-04-2013 06:15 AM
SRMA Problem SAMRecord contig does not match the current reference sequence contig gavin.oliver Bioinformatics 5 07-05-2011 05:28 AM
Contig assembly Ashu Bioinformatics 3 03-08-2011 04:16 AM
Pileup to contig julien Bioinformatics 2 12-02-2009 05:30 AM

Reply
 
Thread Tools
Old 06-24-2012, 02:48 PM   #1
JackieBadger
Senior Member
 
Location: Halifax, Nova Scotia

Join Date: Mar 2009
Posts: 381
Default Contig vs contig or map against contig lib?

Hi,

Can anyone offer some thought in regards to looking for SNPs between two sets of two EST contig libraries?

I have two cDNA contig libraries from sister species and wonder whether it is best to look for diagnostic SNPs between the two via BLAST/BLAT/BFASTing one contig set against the other, or assembling one of the species cDNAs against the contigs from the other?

I have already validated species level SNPs within each from the individual transcript assemblies. I am thinking the best way to look for species level SNPs would be to re-assemble the smaller sized data set against the larger contig library from the other species?

Aligning contigs against each other (in my mind) may cause more complications? (seeing as this is not an annotated scaffold).

Cheers,

J
JackieBadger is offline   Reply With Quote
Old 05-30-2016, 05:34 AM   #2
jorge-bariloche
Junior Member
 
Location: Argentina

Join Date: Oct 2014
Posts: 4
Default old question JackieBadger

Hi JackieBadger
Did you get some answer/solution/tip for this problem? I am more or less in the same situation
thanks


Quote:
Originally Posted by JackieBadger View Post
Hi,

Can anyone offer some thought in regards to looking for SNPs between two sets of two EST contig libraries?

I have two cDNA contig libraries from sister species and wonder whether it is best to look for diagnostic SNPs between the two via BLAST/BLAT/BFASTing one contig set against the other, or assembling one of the species cDNAs against the contigs from the other?

I have already validated species level SNPs within each from the individual transcript assemblies. I am thinking the best way to look for species level SNPs would be to re-assemble the smaller sized data set against the larger contig library from the other species?

Aligning contigs against each other (in my mind) may cause more complications? (seeing as this is not an annotated scaffold).

Cheers,

J
jorge-bariloche 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 10:07 AM.


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