Hello John,
We do get these from UCSC when possible. Mouse sequence files (actually,
all their browser files) are linked from their downloads page. As is the
source code, which includes a set of pre-compiled utilities to convert
between fasta <-> nib <-> 2bit, etc.
http://genome.ucsc.edu and click on left side bar "Downloads"
Hopefully this helps to get you set up, but if you need help with UCSC's
tools, they may be the best contact: gen...@ucsc.edu. If you need more
help with Galaxy's NGS set-up, please let us know,
Best,
Jen
Galaxy team
On 6/16/11 12:04 PM, John David Osborne wrote:
I was wondering how to get a hold of the axt and/or nib files required
by alignseq.loc. It's not mentioned on the local NGA Galaxy setup page.
I was surprised to learn that: "Fetch Sequences -> Extract Genomic DNA"
requires AXT or NIB alignment files in order to extract mouse genomic
DNA from BED file co-ordinates?!
I see some AXT files at UCSC (a lot for human) but the alignment file I
am guessing I needed (for this mm9 genome extraction) is mouse self? I'm
hoping I don't have to generate them all myself, but if I do, I would
love to know how to do it (parameters, etc...).
Any info appreciated,
-John
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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
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