Hi Jen,

Where do you get your AXT or NIB files in order to do the extract genome 
operation? I understand that extract genomic DNA is dependent on those files 
and correct paths/files in AlignSec.loc?

This is for our local instance of Galaxy.

 -John



________________________________________
From: galaxy-user-boun...@lists.bx.psu.edu 
[galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of Jennifer Jackson 
[j...@bx.psu.edu]
Sent: Tuesday, June 21, 2011 10:23 AM
To: Stephen Taylor
Cc: galaxy-u...@bx.psu.edu
Subject: Re: [galaxy-user] Extract Genomic DNA Problem

Hi Stephen,

In your original dataset, there are extra spaces around the tabs.
Where "^I" indicates a tab and "$" indicates an end-of-line character,
the entire datafile looks like this:

chr5 ^I 47258168 ^I 47259240$
chr18 ^I 1938527 ^I 1939965$
chr2 ^I 101973625 ^I 101974007$
chr4 ^I 75653898 ^I 75674045$
chr19 ^I 4258837 ^I 4263299$
chr4 ^I 39330049 ^I 39372715$
chr4 ^I 9606881 ^I 9610083$
chr15 ^I 7264937 ^I 7265599$
chr21 ^I 6659189 ^I 6667015$
chr2 ^I 351239 ^I 352821$

This could have been introduced in many ways, which is why the tools in
Text Manipulation can be so handy. Hopefully this helps!

Best,

Jen
Galaxy team

On 6/21/11 7:58 AM, Stephen Taylor wrote:
> Hi Jeremy,
>
>>
>> This is a formatting issue with your input file; it needs to be
>> tab-delimited but it's not currently. You'll need to:
>>
>> (a) convert spaces to tabs using the "Convert delimiters to Tabs" tool;
>> (b) click on the pencil icon and set the data type to BED.
>
> Thanks, this works, but as a user I cannot see (but obviously you can
> :-)) that there is a difference between my original and the one I did
> step (a) and (b) on. I thought I had uploaded a bed file and converted
> tabs to spaces.
>
> The data is shared here:
>
> http://main.g2.bx.psu.edu/u/stephentaylor/h/test
>
> "Not working" is my original
>
> "Working" is the new data that I did (a) and (b) on.
>
> What did I miss?
>
> Thanks,
>
> Steve
>
>>
>> Best,
>> J.
>>
>> On Jun 21, 2011, at 8:45 AM, Stephen Taylor wrote:
>>
>>> Hi,
>>>
>>> I was trying to extract FASTA sequences using the following tab
>>> separated data for Chicken on the Galaxy Main server:
>>>
>>> chr5 47258168 47259240
>>> chr18 1938527 1939965
>>> chr2 101973625 101974007
>>> chr4 75653898 75674045
>>> chr19 4258837 4263299
>>> chr4 39330049 39372715
>>> chr4 9606881 9610083
>>> chr15 7264937 7265599
>>> chr21 6659189 6667015
>>> chr2 351239 352821
>>>
>>>
>>> I got the following galaxy output:
>>>
>>> ====================================
>>>
>>> 7: Extract Genomic DNA on data 6
>>> empty
>>> format: fasta, database: galGal3
>>> Info: 10 warnings, 1st is: Unable to fetch the sequence from
>>> '47258168' to '1072' for build 'galGal3'.
>>> Skipped 10 invalid lines, 1st is #1, "chr5 47258168 47259240"
>>>
>>> Any ideas what I am doing wrong?
>>>
>>> Thanks,
>>>
>>> Steve
>>> ___________________________________________________________
>>> The Galaxy User list should be used for the discussion of
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>>>
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>>>
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>>
>
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org. Please keep all replies on the list by
> using "reply all" in your mail client. For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
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> please use the interface at:
>
> http://lists.bx.psu.edu/

--
Jennifer Jackson
http://usegalaxy.org/
http://galaxyproject.org/
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

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

  http://lists.bx.psu.edu/
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

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

  http://lists.bx.psu.edu/

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