Cuffdiff and graphics

[plefebvre]

Hi everybody
Now that I could get (painfully ;-)) through the whole analysis of our RNA-seq data using Galaxy, I am quite puzzled on how produced some decent and informative graphic information (exonic vs. intronic hits; number of novel transcripts, differential splicing events etc) starting from this tab files roduced by Cufflinks/Cuffdiff...
Any (simple) hints for somebody working under a Win 7 environment (yes I am not a computer wiz, just a biologist diving into digital biology )??
Thanks!

[jochensupper]

Hi,

we (Genomatix) have released a new tool called Transcriptome Viewer, with the goal to visualize RNA-seq mapping to transcripts, exons and splice-junctions in light of the annotated transcriptome (see attached screenshots). This tool, however, is not based on Tophat/Cufflinks mapping but on our own mapping and RNA-seq approach.

The reason we did this was that we saw the same problem you are pointing out: a lack in visualization tools for RNA-seq workflows. Currently, RNA-seq results are mostly visualized in genome browsers but not in dedicated RNA-seq visualization tools.

Regards

[plefebvre]

Thanks, I guess you are referring to the "mygenomatix" software suite?

[jochensupper]

Right, the Transcriptome Viewer is part of mygenomatix.com.

[pbluescript]

There are command line tools that you can use to do the things you want, but a fairly simple alternative would be to try out SeqMonk for producing some graphics.

http://www.bioinformatics.bbsrc.ac.uk/projects/seqmonk/

There are even some helpful demo videos on Youtube.

[mathew]

Seq monk

How the analysis is done should not matter where one is doing visulaization I mean they may or may not match??