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
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