SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
2b-RAD? does anyone test it? Marianna85 Illumina/Solexa 1 09-12-2013 05:24 AM
RAD-tag or GBS? mcurto Illumina/Solexa 0 09-11-2012 02:55 PM
Qtl semna General 0 10-07-2011 05:28 AM
QTL location? semna Genomic Resequencing 0 10-07-2011 03:48 AM

Reply
 
Thread Tools
Old 02-04-2013, 02:51 AM   #1
pfranchini
Member
 
Location: Cape Town

Join Date: May 2009
Posts: 19
Default RAD-tag QTL annotation

Hi,

We are working on a QTL project and we used markers obtained with the RAD method (100 base pair single-end). We built a linkage map and we found some QTLs with both single markers and Interval mapping analysis. We were wondering about the best method to functionally annotate these QTLs. We have a draft genome for the species we are working on, so I would take advantage of this extra info. Two methods I was thinking (and used in other works) are:

1) Blast the RAD-tags on protein databases (but in our case the short length of the markers, 100bp, could be a problem)

2) Blast the RAD-tags against the draft genome and extract the flanking regions of the blast-hit and annotate these long regions (but how many base pairs are reasonable to extract?)

- What do you think about these methods, advantages and drawbacks?

- Can you suggest me a better way to carry on the functional annotation of the QTLs?

Thanks in advance for your help!

Cheers

Paolo
pfranchini 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 05:05 PM.


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