Annotation File For Cufflinks

Question: Annotation File For Cufflinks

7.3 years ago by

Peng, Tao • 170

Peng, Tao • 170 wrote:

Hi jen and galaxy users, when I try to use cufflinks in GALAXY and select "use reference annotation", I am NOT sure how to get the annotation file in GTF format for cufflinks. I was trying to down-load the annotation file from Illumina donated package in Cufflink website, I am NOT sure this is the right way to go for? Thanks, tao

rna-seq cufflinks • 2.1k views

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modified 7.2 years ago by Gary Xie • 10 • written 7.3 years ago by Peng, Tao • 170

7.3 years ago by

vasu punj • 360

vasu punj • 360 wrote:

If using Ensembl make sure it is properly formatted. Vasu Subject: [galaxy-user] annotation file for cufflinks To: "Jennifer Jackson" <jen@bx.psu.edu>, "galaxy-user" <galaxy- user@lists.bx.psu.edu=""> Date: Tuesday, August 30, 2011, 1:52 PM Hi jen and galaxy users, when I try to use cufflinks in GALAXY and select "use reference annotation", I am NOT sure how to get the annotation file in GTF format for cufflinks. I was trying to down-load the annotation file from Illumina donated package in Cufflink website, I am NOT sure this is the right way to go for? Thanks, tao ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

ADD COMMENT • link written 7.3 years ago by vasu punj • 360

In the cufflink site, they have annotation from ucsc,ncbi & ensemble. not sure which one to download and then load into galaxy? thanks, Tao Sent from my iPhone

ADD REPLY • link written 7.3 years ago by Peng, Tao • 170

7.3 years ago by

Peng, Tao • 170

Peng, Tao • 170 wrote:

Hi I have down-loaded UCSC HG19 annotation files from Cufflinks; Should I just load genes.GTF file (about 100 MB) to galaxy for cufflink analysis? Thanks, tao To: Jennifer Jackson; galaxy-user; Peng, Tao Subject: Re: [galaxy-user] annotation file for cufflinks If using Ensembl make sure it is properly formatted. Vasu Subject: [galaxy-user] annotation file for cufflinks To: "Jennifer Jackson" <jen@bx.psu.edu>, "galaxy-user" <galaxy- user@lists.bx.psu.edu=""> Date: Tuesday, August 30, 2011, 1:52 PM Hi jen and galaxy users, when I try to use cufflinks in GALAXY and select "use reference annotation", I am NOT sure how to get the annotation file in GTF format for cufflinks. I was trying to down-load the annotation file from Illumina donated package in Cufflink website, I am NOT sure this is the right way to go for? Thanks, tao ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

ADD COMMENT • link written 7.3 years ago by Peng, Tao • 170

7.3 years ago by

vasu punj • 360

vasu punj • 360 wrote:

UCSC should work fine. Vasu Subject: RE: [galaxy-user] annotation file for cufflinks To: "vasu punj" <punjv@yahoo.com>, "Jennifer Jackson" <jen@bx.psu.edu>, "galaxy-user" <galaxy-user@lists.bx.psu.edu> Date: Tuesday, August 30, 2011, 10:53 PM Hi I have down-loaded UCSC HG19 annotation files from Cufflinks; Should I just load genes.GTF file (about 100 MB) to galaxy for cufflink analysis? Thanks, tao To: Jennifer Jackson; galaxy-user; Peng, Tao Subject: Re: [galaxy-user] annotation file for cufflinks If using Ensembl make sure it is properly formatted. Vasu Subject: [galaxy-user] annotation file for cufflinks To: "Jennifer Jackson" <jen@bx.psu.edu>, "galaxy-user" <galaxy- user@lists.bx.psu.edu=""> Date: Tuesday, August 30, 2011, 1:52 PM Hi jen and galaxy users, when I try to use cufflinks in GALAXY and select "use reference annotation", I am NOT sure how to get the annotation file in GTF format for cufflinks. I was trying to down-load the annotation file from Illumina donated package in Cufflink website, I am NOT sure this is the right way to go for? Thanks, tao ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

ADD COMMENT • link written 7.3 years ago by vasu punj • 360

7.2 years ago by

Gary Xie • 10

Gary Xie • 10 wrote:

I had a similar question, after i downloaded a bacterial ref genome GFF file and loaded it into Galaxy, the "use reference annotation" feature of Cufflinks kept telling it need to be the GTF file instead, When I check the Cufflinks manual at http://cufflinks.cbcb.umd.edu/manual.html It looks like both GFF and GTF should be ok. Any insight? Gary

ADD COMMENT • link written 7.2 years ago by Gary Xie • 10

This http://bioperl.org/pipermail/bioperl-l/2005-November/020109.html might help to convert gff to gtf. J To: Peng, Tao Cc: galaxy-user Subject: Re: [galaxy-user] annotation file for cufflinks I had a similar question, after i downloaded a bacterial ref genome GFF file and loaded it into Galaxy, the "use reference annotation" feature of Cufflinks kept telling it need to be the GTF file instead, When I check the Cufflinks manual at http://cufflinks.cbcb.umd.edu/manual.html It looks like both GFF and GTF should be ok. Any insight? Gary Hi jen and galaxy users, when I try to use cufflinks in GALAXY and select "use reference annotation", I am NOT sure how to get the annotation file in GTF format for cufflinks. I was trying to down-load the annotation file from Illumina donated package in Cufflink website, I am NOT sure this is the right way to go for? Thanks, tao ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

ADD REPLY • link written 7.2 years ago by Jiannong Xu • 30

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