Hello Anton, Outstanding, thank you very much! Unfortunately, when I try to do that myself, the biomart output file is marked as "html", not "tabular" format. (When I view it, it's indeed HTML), although I chose the Galaxy TSV output format (no other output type is available). That might be a biomart bug. Finally, even if I manage to get plain-text tabular format, how do I convert that to BED or GFF within Galaxy? Best, Alexandre Anton Nekrutenko wrote:

Alexandre:

I made a little movie for you that can be accessible here:

http://screencast.g2.bx.psu.edu/galaxy/BioMart2Galaxy/

There are also other movies (no Festival de Cannes award yet :( ) at this URL:

http://galaxy.psu.edu/screencasts.html

Let me know if you have any trouble.

Thanks,

anton galaxy team

On Jul 25, 2008, at 3:28 AM, Alexandre Gattiker wrote:

...

Hello,

I would like to import features from BioMart into galaxy. However the 'embedded' BioMart view yields an HTML table. How do I convert that to GFF or BED?

Best regards

-- -------------------------------------------------------- Alexandre Gattiker Bioinformatics & Biostatistics Core Facility EPFL School of Life Sciences / Faculté des Sciences de la vie FSV http://people.epfl.ch/Alexandre.Gattiker

_______________________________________________ galaxy-user mailing list galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user

Anton Nekrutenko Asst. Professor Department of Biochemistry and Molecular Biology Center for Comparative Genomics and Bioinformatics Penn State University anton@bx.psu.edu http://nekrut.bx.psu.edu 814.865.4752

-- -------------------------------------------------------- Alexandre Gattiker Bioinformatics & Biostatistics Core Facility EPFL School of Life Sciences / Faculté des Sciences de la vie FSV http://people.epfl.ch/Alexandre.Gattiker

Dear Anton, Sorry for not replying before, I was away. Indeed, I cannot reproduce the bug, but in the meantime BioMart has upgraded to release 50, so I assume that fixed it. So, I can now export tabular format from BioMart. I managed to convert the file to genomic intervals, and from there to BED. For the record, I had to select "interval" format after clicking the pencil icon. Thank you very much for your help Alexandre Anton Nekrutenko wrote:

Dear Alexandre:

We cannot reproduce this error in our environment. Can you send tell us about your OS and browser. Also, if you expand (click) the dataset that is imported from BioMart, you will see an eye icon. If you right click on that icon, you will be able to "Copy link location". Can you send this location to us?

Finally, to convert tab delimited file to genomic intervals (similar to BED or GFF) you need to click on the pencil icon adjacent to the dataset. There, you will be able to set chromosome, start, end, and strand columns.

Please, let me know if you have further issues.

Thanks,

anton galaxy team

-- -------------------------------------------------------- Alexandre Gattiker Bioinformatics & Biostatistics Core Facility EPFL School of Life Sciences / Faculté des Sciences de la vie FSV http://people.epfl.ch/Alexandre.Gattiker