Hi Nicholas, You may be hitting our server limit if you have quite a few locations. We instead recommend that you first create a simple custom BED track of all of your genomic coordinates of interest (for help see http://genome.ucsc.edu/goldenPath/help/customTrack.html). Next go to the Table Browser, make sure your custom track is selected, and then choose the output format "CDS FASTA alignment from multiple alignment". After clicking "get output" you will be taken to a page where you can configure you results.
I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 11/22/10 9:01 PM, Nicholas Price wrote: > Hi, > > I am using a perl script to fetch the alignments. I am using the script > below in a for loop . Sometimes however nothing is returned... For example > if I retrieve $chrom=6 $loc=29105729-29106620 then it does not return the > next one $chrom=6 $loc=28751417-28751785; however if I do them both > separately (not in a for loop) I get an answer...I tried to put the program > to sleep for a while but it doesn't work. What can I do to avoid this > problem ?? > > . > > $url = > "http://genome.ucsc.edu/cgi-bin/hgTables?&clade=mammal&org=Human&db=hg19"; > ."&hgta_group=compGeno&hgta_track=cons46way&hgta_table=multiz46way" > . "&hgta_regionType=range&hgta_outputType=maf&boolshad.sendToGalaxy=0" > . "&hgta_outFileName=&hgta_compressType=none&hgta_doTopSubmit=get+output" > . "&position=chr$chrom%3A$loc"; > $request = HTTP::Request->new('GET', $url); > > $response = $ua->request($request); > > $fckmirnas = $response->content; > > Thank you > > Nicholas > > > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
