Hi John,
Currently, these come from the UCSC Genome Browser's download area.
http://hgdownload.cse.ucsc.edu/downloads.html
AXT files usually come from the primary data source. UCSC provides tools
to create NIB, 2bit, etc. files from fasta (found under "Source"
section, same link as above). If you have other genomes not in their
primarily vertebrate dataset that you want to use with tools that
require these formats, the tools would allow you to create your own.
The Galaxy team, too, has been discussing creating files like this for a
wider range of genomes, but no specific plans are in place yet.
Please let us know if we can help more,
Best,
Jen
Galaxy team
On 6/21/11 10:24 AM, John David Osborne wrote:
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: [email protected]
[[email protected]] On Behalf Of Jennifer Jackson
[[email protected]]
Sent: Tuesday, June 21, 2011 10:23 AM
To: Stephen Taylor
Cc: [email protected]
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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___________________________________________________________
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/
--
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/
--
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/
