Names for genes in RNA-Seq analysis

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Names for genes in RNA-Seq analysis

GANDRILLON OLIVIER
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: [hidden email]

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"

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Re: Names for genes in RNA-Seq analysis

Carl Schmidt
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: [hidden email]

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 :

"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:

 http://lists.bx.psu.edu/

Carl Schmidt
Associate Professor
Animal & Food Sciences
University of Delaware
Newark, DE 19716
051 Townsend Hall
302-831-1334






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Re: Names for genes in RNA-Seq analysis

Jen Hillman-Jackson
In reply to this post by GANDRILLON OLIVIER
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
[hidden email].

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: [hidden email]
>
> 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:
>
>    http://lists.bx.psu.edu/

--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support

Jennifer Hillman-Jackson
http://galaxyproject.org
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Re: Names for genes in RNA-Seq analysis

Jen Hillman-Jackson
In reply to this post by Carl Schmidt
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-zeroes-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, " 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: [hidden email]
>> <mailto:[hidden email]>
>>
>> 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:
>>
>> http://lists.bx.psu.edu/
>
> Carl Schmidt
> Associate Professor
> Animal & Food Sciences
> University of Delaware
> Newark, DE 19716
> 051 Townsend Hall
> [hidden email] <mailto:[hidden email]>
> 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:
>
>    http://lists.bx.psu.edu/

--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support

Jennifer Hillman-Jackson
http://galaxyproject.org
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Re: Names for genes in RNA-Seq analysis

Jen Hillman-Jackson
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-zeroes-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, " 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: [hidden email]
>>> <mailto:[hidden email]>
>>>
>>> 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:
>>>
>>> http://lists.bx.psu.edu/
>>
>> Carl Schmidt
>> Associate Professor
>> Animal & Food Sciences
>> University of Delaware
>> Newark, DE 19716
>> 051 Townsend Hall
>> [hidden email] <mailto:[hidden email]>
>> 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:
>>
>> http://lists.bx.psu.edu/
>

--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support

Jennifer Hillman-Jackson
http://galaxyproject.org
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Re: Names for genes in RNA-Seq analysis

GANDRILLON OLIVIER
In reply to this post by Jen Hillman-Jackson
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 » <[hidden email]> 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: [hidden email]
>>> <mailto:[hidden email]>
>>>
>>> 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:
>>>
>>> http://lists.bx.psu.edu/
>>
>> Carl Schmidt
>> Associate Professor
>> Animal & Food Sciences
>> University of Delaware
>> Newark, DE 19716
>> 051 Townsend Hall
>> [hidden email] <mailto:[hidden email]>
>> 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:
>>
>>    http://lists.bx.psu.edu/
>
>--
>Jennifer Jackson
>http://usegalaxy.org
>http://galaxyproject.org/wiki/Support



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Re: Names for genes in RNA-Seq analysis

Michael Gooch-2
In reply to this post by GANDRILLON OLIVIER
Regarding the GTF files for cuffllinks, how do I obtain one for all
human mRNA that actualy contains gene names rather than accession
numbers. I went to the UCSC table browser but their files contain
accession numbers that I dont know how to decode en-masse.

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Re: Names for genes in RNA-Seq analysis

Jen Hillman-Jackson
In reply to this post by GANDRILLON OLIVIER
Hello Olivier,

When deleting data, it takes the server a short amount of time to
refresh. It may take a bit longer right now since many people are
performing this action at the same time.

For the RNA-seq analysis question, reference annotation GTF files are
used by the Cuff* programs. (These are different than the result GTF
files produced by the programs). For reference annotation GTF files,
there are many sources, including Ensembl and UCSC. Here are links to a
tutorial and an FAQ that can help with your usage question.
http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise
http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq

But, there are many small details to running the tools to get the
optimal results. These types of questions concerning functionality are
best directed to the tool authors at [hidden email]

Take care,

Jen
Galaxy team

On 10/25/11 11:24 PM, GANDRILLON OLIVIER wrote:

> Hello Jennifer
>
>
> Le 26/10/11 02:15, « Jennifer Jackson »<[hidden email]>  a écrit :
>
>> Hello Olivier,
>>
>> Are you using a reference gene annotation GTF file?
>
> Well if I do , I do not know :-)
>
> What I used is first TopHat and then Cufflink. At what stage shall I use
> such a GTF file?
> And additionnaly: where shall I find such a GTF file?
>
> As I understand it: there are tow sources for a GTF file:
> 1. The output from cufflinks generates one (but there is no gene names in
> it..)
> 2. I could get one from Ensembl?
>
> Shall I then use Cuffcompare on the cufflink output?
>
> Best
>
> Olivier
>
> PS: I am now stuck with the galaxy websute that state that I am over my
> disk quota. I have deleted a couple of files but this does not seems to
> help...
>
>

--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support

Jennifer Hillman-Jackson
http://galaxyproject.org
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Re: Names for genes in RNA-Seq analysis

Jen Hillman-Jackson
In reply to this post by Michael Gooch-2
Hello Michael,

The UCSC RefSeq Genes track's has the data:
1) a transcript accession, in column "name"
2) a gene symbol, in column "name2"
but not from the Table Browser's GTF format output, as explained at:
http://genomewiki.ucsc.edu/index.php/Genes_in_gtf_or_gff_format

Ensembl is another data source choice for full functionality, at it
contains: transcript_id, gene_id, and gene_name.

This help from the tool authors is also worth reviewing:
http://cufflinks.cbcb.umd.edu/gff.html

Note that specific questions about these tools can also be directed at:
[hidden email]

Hopefully this helps,

Jen
Galaxy team



On 10/26/11 9:24 AM, Michael Gooch wrote:

> Regarding the GTF files for cuffllinks, how do I obtain one for all
> human mRNA that actualy contains gene names rather than accession
> numbers. I went to the UCSC table browser but their files contain
> accession numbers that I dont know how to decode en-masse.
> ___________________________________________________________
> 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/

--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support

Jennifer Hillman-Jackson
http://galaxyproject.org
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Re: Names for genes in RNA-Seq analysis

GANDRILLON OLIVIER
In reply to this post by Jen Hillman-Jackson
Dear Jennifer


Actually the problem was coming from a non usable Ensembl GTF file. I used
the workflow in
http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq
And remade the Cufflink analysis using the new GTF file as a reference
and, BINGO, it worked.

Thank's for your help

Best

Olivier


Le 28/10/11 20:19, « Jennifer Jackson » <[hidden email]> a écrit :

>Hello Olivier,
>
>When deleting data, it takes the server a short amount of time to
>refresh. It may take a bit longer right now since many people are
>performing this action at the same time.
>
>For the RNA-seq analysis question, reference annotation GTF files are
>used by the Cuff* programs. (These are different than the result GTF
>files produced by the programs). For reference annotation GTF files,
>there are many sources, including Ensembl and UCSC. Here are links to a
>tutorial and an FAQ that can help with your usage question.
>http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise
>http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq
>
>But, there are many small details to running the tools to get the
>optimal results. These types of questions concerning functionality are
>best directed to the tool authors at [hidden email]
>
>Take care,
>
>Jen
>Galaxy team
>
>On 10/25/11 11:24 PM, GANDRILLON OLIVIER wrote:
>> Hello Jennifer
>>
>>
>> Le 26/10/11 02:15, « Jennifer Jackson »<[hidden email]>  a écrit :
>>
>>> Hello Olivier,
>>>
>>> Are you using a reference gene annotation GTF file?
>>
>> Well if I do , I do not know :-)
>>
>> What I used is first TopHat and then Cufflink. At what stage shall I use
>> such a GTF file?
>> And additionnaly: where shall I find such a GTF file?
>>
>> As I understand it: there are tow sources for a GTF file:
>> 1. The output from cufflinks generates one (but there is no gene names
>>in
>> it..)
>> 2. I could get one from Ensembl?
>>
>> Shall I then use Cuffcompare on the cufflink output?
>>
>> Best
>>
>> Olivier
>>
>> PS: I am now stuck with the galaxy websute that state that I am over my
>> disk quota. I have deleted a couple of files but this does not seems to
>> help...
>>
>>
>
>--
>Jennifer Jackson
>http://usegalaxy.org
>http://galaxyproject.org/wiki/Support