Names for genes in RNA-Seq analysis
Hello I am using Galaxy to analyse RNA-seq libraries made from chicken cells. I just groomed my sequences, passed them through TopHat and then Cufflinks. This worked well and in the end I get a list of genes and their respective FPKM values. My only problem is that the names of the genes do not appears in the listing, they are simply reference as "CUFF.1, CUFF.2, " etc… Could you please tell me how I could obtain gene names? (I went through the FAQ and could not get the answer). Sincerely Olivier ----- New mail adress: olivier.gandrillon@univ-lyon1.fr Dr Olivier Gandrillon Centre de Génétique et de Physiologie Moléculaires et Cellulaires UMR CNRS 5534 Université Claude Bernard Lyon I Bat Gregor Mendel (ex 741) 16, rue Raphaël Dubois 69622 Villeurbanne Cedex Phone : 04-72-44-81-90 Fax : 04-72-43-26-85 Web adress : Lab: http://cgphimc.univ-lyon1.fr/spip.php?rubrique33&lang=en Perso: http://www.cgmc.univ-lyon1.fr/Gandrillon/OG/OG1.html "Comment obtenait-il l'adhésion du peuple aux nouveaux mensonges qu'il inventait chaque jour? Précisément parce que c'était des mensonges et précisément parce qu'ils étaient une insulte à la perception. Le peuple était hypnotisé par l'aplomb, ce droit qu'il s'octroyait de contredire l'évidence. Les gens portaient un regard médusé sur un Goebbels déchaîné. Ils voyaient en transparence son souhait énorme de nier le nain boiteux" Tobie Nathan, in "Qui a tué Arlozoroff"
I am also using Galaxy to analyze RNA-seq libraries from chicken. While the names of the genes appear in the Cufflinks output, the FPKM values are all zero. On Oct 20, 2011, at 9:12 AM, GANDRILLON OLIVIER wrote:
Hello
I am using Galaxy to analyse RNA-seq libraries made from chicken cells.
I just groomed my sequences, passed them through TopHat and then Cufflinks.
This worked well and in the end I get a list of genes and their respective FPKM values.
My only problem is that the names of the genes do not appears in the listing, they are simply reference as "CUFF.1, CUFF.2, " etc…
Could you please tell me how I could obtain gene names? (I went through the FAQ and could not get the answer).
Sincerely
Olivier
----- New mail adress: olivier.gandrillon@univ-lyon1.fr
Dr Olivier Gandrillon Centre de Génétique et de Physiologie Moléculaires et Cellulaires UMR CNRS 5534 Université Claude Bernard Lyon I Bat Gregor Mendel (ex 741) 16, rue Raphaël Dubois 69622 Villeurbanne Cedex Phone : 04-72-44-81-90 Fax : 04-72-43-26-85 Web adress : Lab: http://cgphimc.univ-lyon1.fr/spip.php?rubrique33&lang=en Perso: http://www.cgmc.univ-lyon1.fr/Gandrillon/OG/OG1.html
"Comment obtenait-il l'adhésion du peuple aux nouveaux mensonges qu'il inventait chaque jour? Précisément parce que c'était des mensonges et précisément parce qu'ils étaient une insulte à la perception. Le peuple était hypnotisé par l'aplomb, ce droit qu'il s'octroyait de contredire l'évidence. Les gens portaient un regard médusé sur un Goebbels déchaîné. Ils voyaient en transparence son souhait énorme de nier le nain boiteux"
Tobie Nathan, in "Qui a tué Arlozoroff"
___________________________________________________________ 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:
Carl Schmidt Associate Professor Animal & Food Sciences University of Delaware Newark, DE 19716 051 Townsend Hall schmidtc@udel.edu 302-831-1334
Hello Carl, Your question is similar to Olivier's, even though the problem is presenting in a different way. There is most likely a data mismatch problem as explained in my earlier reply to this thread and this prior mailing list question: http://gmod.827538.n3.nabble.com/Cufflinks-reporting-FPKM-values-of-all-zero... Best wishes for your project as well, Jen Galaxy team On 10/20/11 7:32 AM, Carl Schmidt wrote:
I am also using Galaxy to analyze RNA-seq libraries from chicken. While the names of the genes appear in the Cufflinks output, the FPKM values are all zero.
On Oct 20, 2011, at 9:12 AM, GANDRILLON OLIVIER wrote:
Hello
I am using Galaxy to analyse RNA-seq libraries made from chicken cells.
I just groomed my sequences, passed them through TopHat and then Cufflinks.
This worked well and in the end I get a list of genes and their respective FPKM values.
My only problem is that the names of the genes do not appears in the listing, they are simply reference as "CUFF.1, CUFF.2, " etc…
Could you please tell me how I could obtain gene names? (I went through the FAQ and could not get the answer).
Sincerely
Olivier
----- New mail adress: olivier.gandrillon@univ-lyon1.fr <mailto:olivier.gandrillon@univ-lyon1.fr>
Dr Olivier Gandrillon Centre de Génétique et de Physiologie Moléculaires et Cellulaires UMR CNRS 5534 Université Claude Bernard Lyon I Bat Gregor Mendel (ex 741) 16, rue Raphaël Dubois 69622 Villeurbanne Cedex Phone : 04-72-44-81-90 Fax : 04-72-43-26-85 Web adress : Lab: http://cgphimc.univ-lyon1.fr/spip.php?rubrique33&lang=en <http://cgphimc.univ-lyon1.fr/spip.php?rubrique33&lang=en> Perso: http://www.cgmc.univ-lyon1.fr/Gandrillon/OG/OG1.html
"Comment obtenait-il l'adhésion du peuple aux nouveaux mensonges qu'il inventait chaque jour? Précisément parce que c'était des mensonges et précisément parce qu'ils étaient une insulte à la perception. Le peuple était hypnotisé par l'aplomb, ce droit qu'il s'octroyait de contredire l'évidence. Les gens portaient un regard médusé sur un Goebbels déchaîné. Ils voyaient en transparence son souhait énorme de nier le nain boiteux"
Tobie Nathan, in "Qui a tué Arlozoroff"
___________________________________________________________ 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:
Carl Schmidt Associate Professor Animal & Food Sciences University of Delaware Newark, DE 19716 051 Townsend Hall schmidtc@udel.edu <mailto:schmidtc@udel.edu> 302-831-1334
___________________________________________________________ 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:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
There is one more required data point to consider in the GTF file, for full functionality. Specifically, it must also contain the gene_name attribute (in the 9th column), such as: chr1 unknown exon 14362 14829 . - . gene_id "WASH7P"; gene_name "WASH7P"; transcript_id "NR_024540"; tss_id "TSS6960"; Thanks for using Galaxy! Jen On 10/25/11 5:21 PM, Jennifer Jackson wrote:
Hello Carl,
Your question is similar to Olivier's, even though the problem is presenting in a different way. There is most likely a data mismatch problem as explained in my earlier reply to this thread and this prior mailing list question: http://gmod.827538.n3.nabble.com/Cufflinks-reporting-FPKM-values-of-all-zero...
Best wishes for your project as well,
Jen Galaxy team
On 10/20/11 7:32 AM, Carl Schmidt wrote:
I am also using Galaxy to analyze RNA-seq libraries from chicken. While the names of the genes appear in the Cufflinks output, the FPKM values are all zero.
On Oct 20, 2011, at 9:12 AM, GANDRILLON OLIVIER wrote:
Hello
I am using Galaxy to analyse RNA-seq libraries made from chicken cells.
I just groomed my sequences, passed them through TopHat and then Cufflinks.
This worked well and in the end I get a list of genes and their respective FPKM values.
My only problem is that the names of the genes do not appears in the listing, they are simply reference as "CUFF.1, CUFF.2, " etc…
Could you please tell me how I could obtain gene names? (I went through the FAQ and could not get the answer).
Sincerely
Olivier
----- New mail adress: olivier.gandrillon@univ-lyon1.fr <mailto:olivier.gandrillon@univ-lyon1.fr>
Dr Olivier Gandrillon Centre de Génétique et de Physiologie Moléculaires et Cellulaires UMR CNRS 5534 Université Claude Bernard Lyon I Bat Gregor Mendel (ex 741) 16, rue Raphaël Dubois 69622 Villeurbanne Cedex Phone : 04-72-44-81-90 Fax : 04-72-43-26-85 Web adress : Lab: http://cgphimc.univ-lyon1.fr/spip.php?rubrique33&lang=en <http://cgphimc.univ-lyon1.fr/spip.php?rubrique33&lang=en> Perso: http://www.cgmc.univ-lyon1.fr/Gandrillon/OG/OG1.html
"Comment obtenait-il l'adhésion du peuple aux nouveaux mensonges qu'il inventait chaque jour? Précisément parce que c'était des mensonges et précisément parce qu'ils étaient une insulte à la perception. Le peuple était hypnotisé par l'aplomb, ce droit qu'il s'octroyait de contredire l'évidence. Les gens portaient un regard médusé sur un Goebbels déchaîné. Ils voyaient en transparence son souhait énorme de nier le nain boiteux"
Tobie Nathan, in "Qui a tué Arlozoroff"
___________________________________________________________ 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:
Carl Schmidt Associate Professor Animal & Food Sciences University of Delaware Newark, DE 19716 051 Townsend Hall schmidtc@udel.edu <mailto:schmidtc@udel.edu> 302-831-1334
___________________________________________________________ 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:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
Dear Carl After having solved a couple of other problems, I am now to the point where I can: 1.either get the FKPM and no names or 2. have the names and FKPM values to zero (or "OK" ?) So I was wondering whether you had solved this FKPM value problem with chicken you had? Best Olivier Le 26/10/11 02:21, « Jennifer Jackson » <jen@bx.psu.edu> a écrit :
Hello Carl,
Your question is similar to Olivier's, even though the problem is presenting in a different way. There is most likely a data mismatch problem as explained in my earlier reply to this thread and this prior mailing list question: http://gmod.827538.n3.nabble.com/Cufflinks-reporting-FPKM-values-of-all-ze roes-0-tt3183517.html#a3183928
Best wishes for your project as well,
Jen Galaxy team
On 10/20/11 7:32 AM, Carl Schmidt wrote:
I am also using Galaxy to analyze RNA-seq libraries from chicken. While the names of the genes appear in the Cufflinks output, the FPKM values are all zero.
On Oct 20, 2011, at 9:12 AM, GANDRILLON OLIVIER wrote:
Hello
I am using Galaxy to analyse RNA-seq libraries made from chicken cells.
I just groomed my sequences, passed them through TopHat and then Cufflinks.
This worked well and in the end I get a list of genes and their respective FPKM values.
My only problem is that the names of the genes do not appears in the listing, they are simply reference as "CUFF.1, CUFF.2, " etcŠ
Could you please tell me how I could obtain gene names? (I went through the FAQ and could not get the answer).
Sincerely
Olivier
----- New mail adress: olivier.gandrillon@univ-lyon1.fr <mailto:olivier.gandrillon@univ-lyon1.fr>
Dr Olivier Gandrillon Centre de Génétique et de Physiologie Moléculaires et Cellulaires UMR CNRS 5534 Université Claude Bernard Lyon I Bat Gregor Mendel (ex 741) 16, rue Raphaël Dubois 69622 Villeurbanne Cedex Phone : 04-72-44-81-90 Fax : 04-72-43-26-85 Web adress : Lab: http://cgphimc.univ-lyon1.fr/spip.php?rubrique33&lang=en <http://cgphimc.univ-lyon1.fr/spip.php?rubrique33&lang=en> Perso: http://www.cgmc.univ-lyon1.fr/Gandrillon/OG/OG1.html
"Comment obtenait-il l'adhésion du peuple aux nouveaux mensonges qu'il inventait chaque jour? Précisément parce que c'était des mensonges et précisément parce qu'ils étaient une insulte à la perception. Le peuple était hypnotisé par l'aplomb, ce droit qu'il s'octroyait de contredire l'évidence. Les gens portaient un regard médusé sur un Goebbels déchaîné. Ils voyaient en transparence son souhait énorme de nier le nain boiteux"
Tobie Nathan, in "Qui a tué Arlozoroff"
___________________________________________________________ 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:
Carl Schmidt Associate Professor Animal & Food Sciences University of Delaware Newark, DE 19716 051 Townsend Hall schmidtc@udel.edu <mailto:schmidtc@udel.edu> 302-831-1334
___________________________________________________________ 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:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
Hello Olivier, Are you using a reference gene annotation GTF file? This would be required to obtain gene symbols. If yes and this is still an issue, the two things to double check are: 1) the chromosome names between the GTF file (most commonly the problem) and the reference genome and the SAM alignment file are all the same (exactly the same) and 2) the 9th column of the GTF file contains valid gene_id (also commonly incorrect) and transcript_id attributes If this and everything else in the FAQ appear to be in the correct format, it might be time to contact the tool authors for advice at tophat.cufflinks@gmail.com. Best wishes for your project, Jen Galaxy team On 10/20/11 6:12 AM, GANDRILLON OLIVIER wrote:
Hello
I am using Galaxy to analyse RNA-seq libraries made from chicken cells.
I just groomed my sequences, passed them through TopHat and then Cufflinks.
This worked well and in the end I get a list of genes and their respective FPKM values.
My only problem is that the names of the genes do not appears in the listing, they are simply reference as "CUFF.1, CUFF.2, " etc…
Could you please tell me how I could obtain gene names? (I went through the FAQ and could not get the answer).
Sincerely
Olivier
----- New mail adress: olivier.gandrillon@univ-lyon1.fr
Dr Olivier Gandrillon Centre de Génétique et de Physiologie Moléculaires et Cellulaires UMR CNRS 5534 Université Claude Bernard Lyon I Bat Gregor Mendel (ex 741) 16, rue Raphaël Dubois 69622 Villeurbanne Cedex Phone : 04-72-44-81-90 Fax : 04-72-43-26-85 Web adress : Lab: http://cgphimc.univ-lyon1.fr/spip.php?rubrique33&lang=en Perso: http://www.cgmc.univ-lyon1.fr/Gandrillon/OG/OG1.html
"Comment obtenait-il l'adhésion du peuple aux nouveaux mensonges qu'il inventait chaque jour? Précisément parce que c'était des mensonges et précisément parce qu'ils étaient une insulte à la perception. Le peuple était hypnotisé par l'aplomb, ce droit qu'il s'octroyait de contredire l'évidence. Les gens portaient un regard médusé sur un Goebbels déchaîné. Ils voyaient en transparence son souhait énorme de nier le nain boiteux"
Tobie Nathan, in "Qui a tué Arlozoroff"
___________________________________________________________ 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:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
participants (3)
-
Carl Schmidt -
GANDRILLON OLIVIER -
Jennifer Jackson