Hi Brian, I had tried changing the type to wigMaf based on a colleague's suggestion. The problem with that is that when I am completely zoomed out in full display mode, I don't see any elements in my track but if I zoom into the specific region of the alignment then I see the exact alignment. Strangely enough, this is not a problem in dense mode, i.e. it looks fine both zoomed out and zoomed in. I tried changing windowingFunction but that did not help.
Other than that, changing the type to wigMaf is fine by me, but I would ideally like to see all the elements in full mode. Can you reproduce this behavior on your end? Thanks, Saatvik On Tue, Mar 23, 2010 at 3:39 PM, Brian Raney <[email protected]> wrote: > Hey Saatvik, > > I'm able to replicate your error here. The problem is our support for > tracks of type "maf" don't support the use of the trackDb variable > "mafFile" properly. A work-around for this problem is to make the > type of your track "wigMaf" in the trackDb entry (see README in > kent/src/hg/makeDb/trackDb for details). > > I hope this resolves your error. If not, please respond to this > message cc'ing the mail list. > > brian > > On Thu, Mar 18, 2010 at 2:48 AM, Saatvik Agarwal > <[email protected]> wrote: > > Hello, > > > > I am trying to display pairwise alignments generated by BLAT (Genbank > > sequences to hg18) using the MAF format. I like the MAF format since it > is > > pretty close to the UCSC cgi custom track for blat results in that it > shows > > gaps and mismatches graphically. Now if I upload my MAF track (attached) > as > > a custom track, it works fine, but if I load it into our mysql database > (we > > run a personal browser mirror) using hgLoadMaf and add it to my > trackDb.ra > > entry it doesn't work properly. It looks fine when you're zoomed out but > > when I zoom in (to the point where it would normally show the seq. ident > > plot) the browser crashes and just gives me a completely blank webpage. > It's > > obviously this track because if I turn it off everything else works fine. > > > > Any thoughts on what I might be doing wrong? All the examples I saw in > the > > kent src doc were multiple alignments to reference genomes. My MAF aligns > > short sequences from Genbank to a reference genome. > > > > My commands for loading the MAF looks like this: > > > > hgLoadMaf hg18 bejsaGenbankBLAT > > -pathPrefix=/cluster/u/curator/tracks/hg18 -custom > > -loadFile=genbankBLAT.maf > > hgLoadMafSummary -minSize=50 -mergeGap=500 -maxSize=50000 hg18 > > bejsaGenbankBLATSummary /cluster/u/curator/tracks/hg18/genbankBLAT.maf > > > > and my hg18 trackDb.ra entry is as follows: > > > > track bejsaGenbankBLAT > > shortLabel Endogenous enhancers > > longLabel Endogenous (same species) enhancers BLAT > > color 0,255,0 > > priority 1000 > > group regulation > > visibility dense > > mafDot on > > type maf > > mafFile /cluster/u/curator/tracks/hg18/genbankBLAT.maf > > summary bejsaGenbankBLATSummary > > > > Thanks, > > Saatvik > > > > _______________________________________________ > > Genome maillist - [email protected] > > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > > > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
