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.
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: genome(a)ucsc.edu. If you need more
help with Galaxy's NGS set-up, please let us know,
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
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,
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