Hi I have the location of a pseudogene chr11:50129327-50149612 in Human and I am using multiz46way to find orthologous regions in other species. If I use the intersection option "All multiz46way records that have any overlap with UCSC Genes" on your website I get no homology which is the correct answer. However if I use the following URL in my perl script I get an alignment which is the same as when I use "All multiz46way records that have no overlap with UCSC Genes". In other words if I change "hgta_nextIntersectOp=any" to "hgta_nextIntersectOp=none" in my URL I get the same answer, which is not right. Is there something wrong with the URL?
$url = " http://genome.ucsc.edu/cgi-bin/hgTables?&hgta_doIntersectPage=create&hgta_nextIntersectGroup=genes&hgta_nextIntersectTrack " ."=knownGene&hgta_nextIntersectTable=knownGene&hgta_nextIntersectOp=any&hgta_nextMoreThreshold=80&hgta_nextLessThreshold" ."=80&boolshad.hgta_nextInvertTable=0&boolshad.hgta_nextInvertTable2=0&hgta_doIntersectSubmit=submit" ."&clade=mammal&org=Human&db=hg19&hgta_group=compGeno&hgta_track=cons46way&hgta_table=multiz46way" ."&hgta_regionType=range&position=chr11%3A50129327-50149612&hgta_outputType=maf&boolshad.sendToGalaxy=0" ."&boolshad.sendToGreat=0&hgta_outFileName=&hgta_compressType=none&hgta_doTopSubmit=get+output"; Nicholas -- The oppressed become the oppressors Paulo Freire (1921-1997) _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
