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

[Jennifer Jackson]

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 > 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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-- 
Jennifer Jackson

http://galaxyproject.org




--
Jennifer Jackson
http://galaxyproject.org

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

[shamsher jagat]

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  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
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>   http://lists.bx.psu.edu/
>
>
> --
> Jennifer Jacksonhttp://galaxyproject.org
>
>
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Re: [galaxy-dev] Extracting bacterial seq from cordinates

[Jennifer Jackson]

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


___
Please keep all replies on the list by using "reply all"
in your mail client.  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

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[galaxy-dev] Extracting bacterial seq from cordinates

[shamsher jagat]

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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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

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