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,