Good Morning Sina: If you want to find where some feature intersects with the repeat masker track on any genome, you can use the table browser and run an intersection of your features with the repeat masker track.
The repStart,repEnd,repLeft are what you described in earlier email. They are coordinates on the actual repeat sequence itself. This has nothing to do with the genome. You can read all about repeat masker in the description page of that track and the repeat masker documentation. --Hiram ----- Original Message ----- From: "Sina Vivekanandan" <[email protected]> To: "Hiram Clawson" <[email protected]> Cc: [email protected] Sent: Sunday, November 21, 2010 10:03:48 PM GMT -08:00 US/Canada Pacific Subject: RE: [Genome] Regarding repeat masked tables (human) in ucsc Hi Hiram Firstly, thanks for your time!!...And yes, it is the same genome. What I have is the comparison results (in terms of exact sequence matches using the tool mummer) of 2 genomes, one being hg18. Since I performed these comparisons without repeat masking the hg18 genome, I have obtained matches which falls within the repeats as well. Now what I intend to do is to look into this repeat masker data given on UCSC and remove the matches which fall within the reported repeat regions. So to do this, I need to know the coordinates where the repeats fall. So you mean to say, the exact locations of the repeats are exactly genoName, genoStart and genoEnd. Then what do the coordinates on the columns repStart, repEnd and repLeft provide?? Thanks in advance Sina K V _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
