Hello Qianli,

This appears to be the same data as submitted as a recent bug? Converting the query coordinates to BED format is still the recommendation. This should be a good solution for most, if not all, of your prior Extract tool failures and is a good method overall.


First "Convert Formats -> GFF-to-BED", followed by clicking on the pencil icon to assign the last three columns on the "Edit Attributes" form, in particular you will want to get strand assigned, so that c4 = name, c5 = score, and c6 = strand. The datatype will be bed. Then extract using your custom genome and the sequence will be titled by the region coordinates.

Best,

Jen
Galaxy team

On 5/29/12 11:58 AM, Qianli Shen wrote:
Hi

I want to fetch sequence from soybean genome, according to a gff file. My gff3 file and genome file are attached to the email, because it is not easy to recongnize the format if I paste it in the email. And it keeps reporting the error:

An error occurred running this job: Traceback (most recent call last):
File "/galaxy/home/g2main/galaxy_main/tools/extract/extract_genomic_dna.py", line 288, in <module>
if __name__ == "__main__": __main__()
File "/galaxy/home/g2main/galaxy_main/tools/extract/extract_genomic_dna.py"


Could you please tell me where is the problem?


Best
Qianli





___________________________________________________________
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://galaxyproject.org

___________________________________________________________
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/

Reply via email to