Hi Javeed, We added links to the page, as you suggested. Scroll down to:
start -- The start of the aligning region in the source sequence. This is a zero-based number. If the strand field is '-' then this is the start relative to the reverse-complemented source sequence (see Coordinate Transforms). Please let us know if you think they would be helpful in a different location! And thank you for the suggestion. -- Brooke Rhead UCSC Genome Bioinformatics Group On 01/31/11 09:46, Jaaved Mohammed wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
