Can we also fetch virus file from some sources like this? Thanks Kanwar On Mon, Nov 26, 2012 at 4:25 AM, Joachim Jacob <joachim.jacob@vib.be> 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 <mira.bisso@dasmaninstitute.org>>*

**

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Thanks Jeremy, Are there any resources linked with Galaxy for viral genome seq annotation ? Kanwar On Mon, Nov 26, 2012 at 11:36 AM, Jeremy Goecks <jeremy.goecks@emory.edu>wrote:

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>*

**

___________________________________________________________

Please keep all replies on the list by using "reply all"

in your mail client. To manage your subscriptions to this

and other Galaxy lists, please use the interface at:

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___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:

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___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:

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