Hi Hiram, Thanks for pointing out this wiki. Since the MAF format description on the USCS browser help-page does not make this interpretation explicit (see http://genome.ucsc.edu/FAQ/FAQformat.html#format5), may I suggest to put a link to this wiki there? I think it would benefit lots of folks out there.
Thanks, Jaaved -----Original Message----- From: Hiram Clawson [mailto:[email protected]] Sent: Monday, January 31, 2011 12:11 PM To: Jaaved Mohammed Cc: [email protected] Subject: Re: [Genome] Insect MAF file coordinate-sequence disagreement See also: http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms Brian Raney wrote: > We realize that these coordinate systems can be confusing, but using > these systems internally makes it easier to avoid different code for > alignments on the different strands. > > On Thu, Jan 27, 2011 at 2:15 PM, Jaaved Mohammed <[email protected]> wrote: >> Hello, >> >> I am seeing numerous discrepancy between the sequences and coordinates in >> the insect 15-way multiple-alignment files >> (http://hgdownload.cse.ucsc.edu/goldenPath/dm3/multiz15way/) primarily for >> D. ananassae and D. virilus. Hopefully I can explain this as concisely as >> possible, however, let me know how I can clarify: _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
