The Galaxy team recommends using the gene annotations from the iGenomes project: http://tophat.cbcb.umd.edu/igenomes.html

To avoid downloading the complete package for humans, you can find (and import or download) the hg19 gene annotation from the 'iGenomes' data library on our public server: 

http://tinyurl.com/cdwq5od

Best,

J.

On Nov 26, 2012, at 7:25 AM, Joachim Jacob wrote:

You can use 'Get data' --> 'UCSC Main' to fetch an GTF (gene transfer format) format of your species of interest, Human in this case. I tend to use the Ensembl genes track (from the Genes and gene prediction tracks).

Make sure you use GTF as output, and send to Galaxy!

Cheers,
Joachim

Joachim Jacob, PhD

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

On 11/26/2012 01:07 PM, Dr. Mira A. Bisso wrote:

Dear help;

How to get the human annotation file for RNAseq analysis, for mapping by BWA and for RNAseq analysis, on Cufflinks and cuffdiff tools on galaxy?

Mira

Thanks

*image001*

**

*Mira Bosso, M.Sc, B.D.S*

*Research associate*

*Pancreatic Islet Biology and Transplantation Unit*

*P.O.Box 1180, Dasman 15462, Kuwait

Phone:  +965 2224 2999 Ext.2803*

*Mob: +96599500197 *

*Email: mira.bisso@dasmaninstitute.org <mailto:mira.bisso@dasmaninstitute.org>*

**

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