Hello Hong,

To let you know, the Extract tool will work with any fasta dataset in your history as a "Custom reference genome". Instructions are here: http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome

Take care,

Jen Galaxy team

On 4/4/12 10:37 AM, hongxu wrote:

Hi Jen,

Thank you for the reply. I'll try BED6 and see in Galaxy. I would also want to try ENSEMBL API, because one of our publication is based on ENSEMBL database.

Best, Hong Xu

...

From: Jennifer Jacksonjen@bx.psu.edu Reply-To: To: hongxuhongxu@zju.edu.cn Subject: Re: [galaxy-user] Galaxy Server running error in fetching sequences Date: Wed, 04 Apr 2012 07:14:27 -0700

Hello Hong,

There is likely a problem with the formatting of your input file. BED and GFF format are very different, and this may be the problem. You will want to input a strict "BED6" file to this tool:

http://wiki.g2.bx.psu.edu/Learn/Datatypes#Bed

http://wiki.g2.bx.psu.edu/Learn/Datatypes#GFF

If you continue to have problems, please submit a bug report by clicking on the green bug icon for the red error dataset. This allows us to access your data/job privately and provide help/feedback.

Best,

Jen Galaxy team

...

On Apr 3, 2012, at 4:37 PM, xu hong wrote:

...

Hi Anton,

I'm a biological student using Galaxy sever to fetch sequences in fasta format for our bioinformatics data analysis. First, I uploaded our BED file(I think there is no significant difference from the GFF format defined in Galaxy/UCSC), and then use "Fetch Sequences" function in Galaxy Server. However, I got the following error:

"2: Extract Genomic DNA on data 1 0 bytes 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

...

...

...

f __name__ == "__main__": __main__() File "/galaxy/home/g2main/galaxy_main/tools/extract/extract_genomic_dna.py" "

Could you help me configure out what's wrong with my analysis or could you get the fasta file I want for me?

Attached is the BED file(based on hg18) I uploaded to Galaxy server in psu.

Thanks.

Beg your reply.

Best Hong Xu Zhejiang University,China

...

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