How to visualize mapped RNAseqs and annotations?

JonB · 09-25-2012, 12:42 AM

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

rohitngs · 09-25-2012, 12:52 AM

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

severin · 09-25-2012, 05:28 AM

GBrowse2 is my flavor of choice.

mbayer · 10-01-2012, 02:04 AM

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

JonB · 10-01-2012, 02:19 AM

Thanks!
I tried Tablet and it works fine. Only had to increase the memory in order to import the ace file.

Dolphin22 · 10-01-2012, 02:27 AM

Hi there,

you could also use Integrated Genome Browser
http://bioviz.org/igb/

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09-25-2012, 12:42 AM	#1
JonB Member Location: Norway Join Date: Jan 2010 Posts: 83	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

09-25-2012, 12:52 AM	#2
rohitngs Member Location: Hyd Join Date: Jul 2012 Posts: 14	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.

09-25-2012, 05:28 AM	#3
severin Genome Informatics Facility Location: Iowa @isugif Join Date: Sep 2009 Posts: 105	visualization GBrowse2 is my flavor of choice.

10-01-2012, 02:04 AM	#4
mbayer Member Location: Dundee, Scotland Join Date: Mar 2009 Posts: 29	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

10-01-2012, 02:19 AM	#5
JonB Member Location: Norway Join Date: Jan 2010 Posts: 83	Thanks! I tried Tablet and it works fine. Only had to increase the memory in order to import the ace file.

10-01-2012, 02:27 AM	#6
Dolphin22 Member Location: Bielefeld Join Date: Jul 2012 Posts: 24	Hi there, you could also use Integrated Genome Browser http://bioviz.org/igb/