SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
How to visualize RPKM in a browser? dmotti Bioinformatics 4 08-28-2015 11:07 AM
Hot to calculate coverage on a 454 targeted region sequenced ? Giorgio C Bioinformatics 9 10-23-2012 02:06 PM
visualize gmap results Kennels Bioinformatics 0 02-14-2012 02:49 PM
Best way to visualize raw reads, and RPKMs? Bradburne Bioinformatics 6 08-23-2010 12:27 AM
How to visualize bowtie output? caspase Illumina/Solexa 2 11-16-2009 11:15 PM

Reply
 
Thread Tools
Old 09-25-2012, 12:42 AM   #1
JonB
Member
 
Location: Norway

Join Date: Jan 2010
Posts: 83
Default How to visualize mapped RNAseqs and annotations?

I have a bunch of supercontigs with RNAseqs mapped to them in an ace file. In a gtf file I have the annotations for these supercontigs. How can I display the contigs with the mapped reads and the annotations at the same time?
I am currently using Geneious Pro.

Thanks!

Jon

Last edited by JonB; 09-25-2012 at 12:45 AM. Reason: Spelling mistake
JonB is offline   Reply With Quote
Old 09-25-2012, 12:52 AM   #2
rohitngs
Member
 
Location: Hyd

Join Date: Jul 2012
Posts: 14
Default Re: How to visualize mapped RNAseqs and annotations?

Use any genome visualizer such as the IGV - Integrative Genomics Viewer.
Its stand-alone and quite simple.

But if you're gonna try and make manipulations later, NCBI genomics workbench is a better go.


Regards,
Rohit

Last edited by rohitngs; 09-25-2012 at 12:57 AM.
rohitngs is offline   Reply With Quote
Old 09-25-2012, 05:28 AM   #3
severin
Genome Informatics Facility
 
Location: Iowa @isugif

Join Date: Sep 2009
Posts: 105
Default visualization

GBrowse2 is my flavor of choice.
severin is offline   Reply With Quote
Old 10-01-2012, 02:04 AM   #4
mbayer
Member
 
Location: Dundee, Scotland

Join Date: Mar 2009
Posts: 29
Default

Hi Jon,

try Tablet (http://bioinf.scri.ac.uk/tablet/). It takes ace files and you can import annotation as tracks in GFF format (if you have annotation in your GTF file you may need to tweak this slightly but as far as I know the rest of the file format is identical between the two).

If your ace file is really big you may want to consider BAM instead, if that's an option -- there are no size contraints with that format.

cheers

Micha
mbayer is offline   Reply With Quote
Old 10-01-2012, 02:19 AM   #5
JonB
Member
 
Location: Norway

Join Date: Jan 2010
Posts: 83
Default

Thanks!
I tried Tablet and it works fine. Only had to increase the memory in order to import the ace file.
JonB is offline   Reply With Quote
Old 10-01-2012, 02:27 AM   #6
Dolphin22
Member
 
Location: Bielefeld

Join Date: Jul 2012
Posts: 24
Default

Hi there,

you could also use Integrated Genome Browser
http://bioviz.org/igb/
Dolphin22 is offline   Reply With Quote
Reply

Tags
ace, geneious, gtf, rnaseq, visualization

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 05:49 AM.


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