Thanks a lot Jennifer, Will try what u suggested. With Regards, ---------------- Ambarish Biswas, University of Otago Department of Biochemistry, Dunedin, New Zealand, Tel: +64(22)0855647 Fax: +64(0)3 479 7866 On Fri, Feb 3, 2012 at 10:21 AM, Jennifer Jackson <jen@bx.psu.edu> wrote:

Hello Ambarish,

On 2/1/12 6:42 PM, ambarish biswas wrote:

...

Hi,

when I try to fetch sequence for SacCer3 using UCSC Main table Browser,

Are you using "Get Data -> UCSC Main", to access the UCSC Main table browser and the sacCer3 database? If so, and errors are coming up in the Table Browser, then the UCSC team should be contacted. http://genome.ucsc.edu/**contacts.html<http://genome.ucsc.edu/contacts.html>

However, the rest of your comments suggest that you are instead using other tools, maybe two? These Galaxy tools?

Fetch Sequences -> Extract Genomic DNA & Fetch Alignments -> Extract MAF Blocks

The sacCer3 genome has not (yet) been added as a native genome. http://wiki.g2.bx.psu.edu/**Support#Missing_reference_**genome<http://wiki.g2.bx.psu.edu/Support#Missing_reference_genome> For now, you will want to download this genome from UCSC in fasta format and upload it into Galaxy and use it as a Custom genome. The same can be done with MAF data in .wig format with many of the MAF tools.

In the future, it is best not to open tickets at bitbucket for tool errors or questions. http://wiki.g2.bx.psu.edu/**Support#Error_from_tools<http://wiki.g2.bx.psu.edu/Support#Error_from_tools> Instead, please send questions to the mailing list and we can discussion potential options and open tickets if that seems appropriate. Genome requests are tracked outside of bitbucket and I can let you know that sacCer3 is on our list, but not prioritized yet.

Hopefully this helps,

Best,

Jen Galaxy team

I received the following error:

...

"An error occurred running this job: No sequences are available for 'sacCer3', request them by reporting this error."

I noticed that, It's possible to extract sequence for SacCer2, but again none of the SacCer2 or SacCer3 has allowed

"Fetch Alignments->Extract MAF Blocks"

Is it a bug or compatibility issue? Hope this can be fixed or else will be a problem for me.

With Regards, ---------------- Ambarish Biswas, University of Otago Department of Biochemistry, Dunedin, New Zealand, Tel: +64(22)0855647 Fax: +64(0)3 479 7866

On Thu, Feb 2, 2012 at 3:01 PM, Bitbucket <issues-reply@bitbucket.org <mailto:issues-reply@**bitbucket.org <issues-reply@bitbucket.org>>> wrote:

--- you can reply above this line ---

Issue 710: An error occurred running this job- No sequences are available for sacCer3 https://bitbucket.org/galaxy/**galaxy-central/issue/710/an-** error-occurred-running-this-**job-no<https://bitbucket.org/galaxy/galaxy-central/issue/710/an-error-occurred-running-this-job-no>

ambarishbiswas on Thu, 2 Feb 2012 03:01:34 +0100:

Changes: component: nothing -> tools

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