Hello, The format is incorrect for the interval file - the "chromosome" field (c1, or the first field) should be the same as the "identifier" (the ">" line) in the fasta file. In your case, this is: AF148805 Change what you have assigned as "Chr1" to be "AF148805" to make the correction. Take care, Jen Galaxy team On 12/19/12 4:19 PM, shamsher jagat wrote:
Jen,
I have also shared history with you File 27 and 32 are fetching empty seq file. I think since bacterial genome is not having any Chr that may be the problem, I tried all option just coordinates; Chr1 however the out put is empty.
Thanks
Kanwar
On Wed, Dec 19, 2012 at 10:07 AM, Jennifer Jackson <jen@bx.psu.edu <mailto:jen@bx.psu.edu>> wrote:
Hello,
Both datasets can be loaded and the "custom reference genome" option used with the tool 'Fetch Sequences -> Extract Genomic DNA". Details about custom genomes are grouped here in our: http://wiki.galaxyproject.org/Support#Custom_reference_genome
To be specific, on the "Extract" tool form, you will use the option: "Source for Genomic Data:" as "History", then for the new menu option "Using reference file:", select the fasta dataset of your genome from your active history.
If you have trouble, be sure to double check that your formats match those required by the tool (listed on tool's form). Detailed custom genome troubleshooting help is in the wiki above and file format troubleshooting help is here, including links to data specifications: http://wiki.galaxyproject.org/Support#Troubleshooting_tool_errors (start here, more help in following sections, same wiki)
Best,
Jen Galaxy team
On 12/19/12 8:19 AM, shamsher jagat wrote:
I have a bacterial genome from ncbi and woulld like to extract seq from the corresponding fasta file of bacterial genome. Since i have list of coordinates so would not be possible to extract one by one. Is there any interface within galxy that i can use.
Thanks
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