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(a)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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