GSNAP - another mapping tool

[Markus Schroeder]

Hi all,

this is GMAP/GSNAP, the mapping tool I mentioned earlier today.
Developed by Genentech and used for all their sequencing projects:

Paper:
GMAP (2005) -
http://bioinformatics.oxfordjournals.org/content/21/9/1859.full
GSNAP (2010) -
http://bioinformatics.oxfordjournals.org/content/26/7/873.full

Web: http://research-pub.gene.com/gmap/

Also featured in the EBI review about mapping tools:
http://bioinformatics.oxfordjournals.org/content/28/24/3169.full

Best,
Markus

[Markus Schroeder]

And this is the RABT feature of TopHat:

http://bioinformatics.oxfordjournals.org/content/27/17/2325

Bioinformatics. 2011 Sep 1;27(17):2325-9. doi: 10.1093/bioinformatics/btr355. Epub 2011 Jun 21.

Identification of novel transcripts in annotated genomes using RNA-Seq.

Roberts A, Pimentel H, Trapnell C, Pachter L.

Source

Department of Computer Science, UC Berkeley, Berkeley, CA, USA.

I think Ines looked into this one as well if anyone has questions!

Best,
Markus

[Yue Fan]

Hi,

This is the cbio portal for easily accessing the TCGA datasets:

http://www.cbioportal.org/public-portal/

There is also an R package:

http://www.cbioportal.org/public-portal/cgds_r.jsp

Thanks.

Regards

Yue

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