Re: [galaxy-dev] Extracting bacterial seq from cordinates

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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