SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
RNA-Seq: RSEQtools: A modular framework to analyze RNA-Seq data using compact, anonym Newsbot! Literature Watch 1 02-27-2013 03:16 AM
Plotting ChIP-seq read profiles relative to genomic features Gilman85 Bioinformatics 7 12-07-2012 09:45 AM
Help with plotting ngs (small RNA seq) data Ami Bioinformatics 4 06-07-2011 12:12 AM
RNA-Seq: Length Bias Correction for RNA-seq Data in Gene Set Analyses. Newsbot! Literature Watch 0 01-22-2011 02:02 AM
bacterial RNA-seq workbench options? rnaseq RNA Sequencing 0 12-06-2010 11:47 AM

Reply
 
Thread Tools
Old 11-24-2010, 11:11 PM   #1
sujata
Junior Member
 
Location: USA

Join Date: Nov 2010
Posts: 2
Default What are the available best options for plotting RNA-seq data?

Hello

I was just wondering what are the available best options available for plotting and visualizing RNA-seq data.

thanks in advance
sujata
sujata is offline   Reply With Quote
Old 11-25-2010, 10:39 PM   #2
GKM
Member
 
Location: Pasadena, CA

Join Date: May 2009
Posts: 45
Default

You can't really "plot" the RNA-Seq data, you can display the alignments or read densities on any of the multiple currently available genome browsers. Or you can plot specific things about the data in myriad ways...

Last edited by GKM; 11-25-2010 at 11:07 PM.
GKM is offline   Reply With Quote
Old 11-25-2010, 11:06 PM   #3
NicoBxl
not just another member
 
Location: Belgium

Join Date: Aug 2010
Posts: 264
Default

artemis is fine
NicoBxl is offline   Reply With Quote
Old 11-26-2010, 04:30 AM   #4
colindaven
Senior Member
 
Location: Germany

Join Date: Oct 2008
Posts: 415
Default

We like IGB, it does the job well and is very flexible. Others include Jbrowse, IGV etc -- look in the software wiki.

Tablet is great, but support for annotations is still in development ...
colindaven is offline   Reply With Quote
Old 11-27-2010, 01:33 AM   #5
Wolfgang Huber
Senior Member
 
Location: Heidelberg, Germany

Join Date: Aug 2009
Posts: 109
Default

For totally flexible plotting and associated computations on the data (but using a programmatic interface with a steep learning curve), the GenomeGraphs package from Bioconductor, and the associated data manipulation and integration tools:
http://www.bioconductor.org/help/wor...put-sequencing
__________________
Wolfgang Huber
EMBL
Wolfgang Huber is offline   Reply With Quote
Old 11-27-2010, 11:28 AM   #6
bioinfosm
Senior Member
 
Location: USA

Join Date: Jan 2008
Posts: 482
Default

Quote:
Originally Posted by Wolfgang Huber View Post
For totally flexible plotting and associated computations on the data (but using a programmatic interface with a steep learning curve), the GenomeGraphs package from Bioconductor, and the associated data manipulation and integration tools:
http://www.bioconductor.org/help/wor...put-sequencing
Is there an RNA-Seq specific workflow within the bioconductor package?
bioinfosm is offline   Reply With Quote
Old 11-28-2010, 01:58 AM   #7
simonandrews
Simon Andrews
 
Location: Babraham Inst, Cambridge, UK

Join Date: May 2009
Posts: 871
Default

SeqMonk (which we develop, so I'm slightly biased!) can plot spliced alignments and you can use it either as a simple data browser, or calculate and plot quantitated data. You can import a SAM file straight from tophat.

There's a section in our training manual which briefly discusses options for RNA-Seq (p40)
simonandrews is offline   Reply With Quote
Old 11-29-2010, 12:23 AM   #8
simonandrews
Simon Andrews
 
Location: Babraham Inst, Cambridge, UK

Join Date: May 2009
Posts: 871
Default

If it's any help I've just put up a video showing a simple RNA-Seq analysis in SeqMonk - you can see how the data looks and some of the simple tools for identifying differential expression.
simonandrews is offline   Reply With Quote
Old 12-06-2010, 09:46 AM   #9
bioinfosm
Senior Member
 
Location: USA

Join Date: Jan 2008
Posts: 482
Default

Hey thats great!

Thanks for the video ..
__________________
--
bioinfosm
bioinfosm 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 01:57 PM.


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