To get the whole chromosome graph on the maf display, run the hgLoadMafSummary command on your maf file and into a summary table of your name choice, e.g.: yourTableNwaySummary. Name this table in the trackDb entry to cause it to be used:
summary yourTableNwaySummary Note the many examples of this type of specification in the trackDb.ra files under any of our genomes that have a multiple alignment conservation track. --Hiram Saatvik Agarwal wrote: > 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 > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
