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: genome@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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