[galaxy-dev] how to get annotation files for rna-seq
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.bi...@dasmaninstitute.orgmailto:mira.bi...@dasmaninstitute.org inline: image001.png___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] how to get annotation files for rna-seq
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.bi...@dasmaninstitute.org mailto:mira.bi...@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: http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] how to get annotation files for rna-seq
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.ja...@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.bi...@dasmaninstitute.org mailto:mira.bisso@** dasmaninstitute.org mira.bi...@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: http://lists.bx.psu.edu/ __**_ 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: http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] how to get annotation files for rna-seq
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. ___ 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: http://lists.bx.psu.edu/
