SEQanswers

Go Back   SEQanswers > Applications Forums > Metagenomics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Appropriate to assign taxonomy to OTUs? primordialsoup77 Bioinformatics 0 12-03-2013 06:31 PM
Bacterial species definition / OTUs rhinoceros Metagenomics 1 10-24-2013 04:31 AM
Comparing sequences between themselves ramirob Bioinformatics 4 02-16-2013 01:05 AM
How are you comparing assemblies? Hobbe Bioinformatics 0 02-17-2011 10:38 PM
Comparing Transcriptomes poregide Bioinformatics 1 08-25-2010 11:23 PM

Reply
 
Thread Tools
Old 03-17-2015, 05:38 AM   #1
JenBarb
Member
 
Location: Bethesda, MD

Join Date: Oct 2010
Posts: 47
Default Comparing OTUs from different V regions?

Hello,
I have data generated from using 6 different primers which target 6 different V regions of the 16s gene from the same samples. I am wondering if anyone has any advice on how to compare or combine the results from the different regions in order to come up with a consensus result?

I know that this is a tricky question but I am just curious if anyone else is doign this and what advice they might have for this.
Thanks,
Jen
JenBarb is offline   Reply With Quote
Old 04-09-2015, 11:49 AM   #2
thermophile
Senior Member
 
Location: CT

Join Date: Apr 2015
Posts: 243
Default

the only way to compare across regions is to just taxonomically identify the sequences against the same database and compare the results. Depending on what your samples are and how well your organisms are represented in the databases, the results could be between mildly interesting and a waste of time. (I tried something like this on 454 sequenced deep ocean samples v8-9 vs v1-3, it was a waste of time). If you are trying to determine what region to use for a larger study, you're better off creating a database of full length sequences that are representative of your communities and doing the comparison in silico
thermophile 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 11:29 PM.


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