SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Need help annotating.. shyam_la Bioinformatics 9 06-15-2012 04:06 AM
Annotating variants using Annovar question Phantom123 Bioinformatics 5 03-25-2012 08:16 PM
Annotating indels anjulka Bioinformatics 4 03-22-2012 08:13 AM
Annotating reference followed by mapping? tboothby Bioinformatics 0 12-22-2011 10:21 AM

Reply
 
Thread Tools
Old 03-04-2013, 06:30 PM   #1
LouiseT
Member
 
Location: Melbourne, Australie

Join Date: Feb 2013
Posts: 11
Default Annotating a complex list of variants

Hi everybody
I am trying to annotate identified variants obtained from a number of methods (so I have both CNVs, point mutations, CpG sites e.g.). I would like to annotate with all known functional elements both coding and noncoding RNA, TF binding sites e.g.

The best way I can see is to download annotation files and use fx. BedOps to identify functional elements that overlap with my variants.

If anyone has a better idea or know of a software that can handle the complexity of my data please send me a hint.

I have downloaded annotation files from UCSC table browser. If you know of sites containing info that can compliment this information please let me know of that to.

Also if you know of a database which include non-coding elements in enrichment analysis and pathway identification I could use some guidance.
LouiseT is offline   Reply With Quote
Reply

Tags
annotate, complex variants, data integration

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 07:00 PM.


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