Re: RNAseq Helicobacter pylori

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Re: RNAseq Helicobacter pylori

Jen Hillman-Jackson
Hello Kaisa,

These are related formats and generally differ only in the 9th column,
which is important for data labeling with these tools.
The formats as well as some utilities to help with parsing are
documented here:
http://cufflinks.cbcb.umd.edu/gff.html
Also note the help email: [hidden email]

For the data files in GFF, you may try contacting the data source and
asking for help. It is possible that the attributes needed to create a
GTF file exist in other files and the data could be transformed (outside
of Galaxy).

Hopefully this helps,

Jen
Galaxy team


On 11/2/11 4:58 AM, Kaisa Thorell wrote:

> Hi!
>
> I tried to do as you described but when I come to the tophat/cufflinks analysis I can only find .gff files for the strains that I'm working with and no .gtf files. What is the difference between them and is there any way to convert the .gff into .gtf or does one need any additional information?
>
> Best regards
>
> Kaisa
>
> ________________________________________
> From: [hidden email] [[hidden email]] on behalf of Jennifer Jackson [[hidden email]]
> Sent: 28 October 2011 19:42
> To: Benoit HENNUY
> Cc: [hidden email]
> Subject: Re: [galaxy-user] RNAseq Clostridium butyricum
>
> Hello,
>
> The quickest way to use this genome is to load it into your history in
> fasta format. Use FTP, as described here:
> http://wiki.g2.bx.psu.edu/Learn/Upload%20via%20FTP
>
> Then, use the "NGS: RNA Analysis" tool set's first step TopHat with the
> option "Will you select a reference genome from your history or use a
> built-in index?: Use one from the history". Most of Galaxy's mapping
> tools have this option, although it may be named slightly differently on
> the tool forms.
>
> A double check that your uploaded reference genome has the same exact
> identifiers present in any reference annotation GTF file you plan to use
> in later steps is a good idea. This will ensure that the TopHat mapping
> results will be interpreted correctly by the Cuff* tools. Even minor
> differences in chromosome/scaffold names will cause problems and it is
> easier to align the naming conventions up-front.
>
> Tutorial and FAQ:
> 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
>
> Best wishes for your project,
>
> Jen
> Galaxy team
>
> On 10/28/11 7:38 AM, Benoit HENNUY wrote:
>> Hi,
>> I would like to use Galaxy with RNAseq data generated from "Clostridium
>> butyricum" species. Please, could you include this genome in your list ?
>> Thank you in advance
>>
>> Best regards
>> Benoit HENNUY
>> ___________________________________________________________
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>
> --
> Jennifer Jackson
> http://usegalaxy.org
> http://galaxyproject.org/wiki/Support
> ___________________________________________________________
> 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