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.orgmailto:mira.bisso@dasmaninstitute.org
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:
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>*
**
______________________________**_____________________________ 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:
______________________________**_____________________________ 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:
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:
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:
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:
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.eduwrote:
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:
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:
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:
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:
Thanks Jeremy, Are there any resources linked with Galaxy for viral genome seq annotation ?
I'm not aware of any viral genome annotations resources integrated into Galaxy, but NCBI (and others) have virus gene annotations that you upload into Galaxy and use.
Best, J.
galaxy-dev@lists.galaxyproject.org