Hi Akshay, The Genome Browser hosted by UCSC (found at http://genome.ucsc.edu/) does not host the A. thaliana genome. There are some sites that mirror the UCSC Genome Browser and include additional genomes, and they may or may not keep their software up-to-date with our releases, so some of the newer file formats may not be supported on their websites. I see a couple of possible sites you may be looking at:
http://altair.dartmouth.edu/cgi-bin/hgGateway?org=A.+thaliana&db=araTha9 http://shenlab.sols.unlv.edu/cgi-bin/hgGateway?org=A.+thaliana&db=arab1 I suggest contacting them directly to determine what file formats they currently support. -- Brooke Rhead UCSC Genome Bioinformatics Group On 12/8/11 2:25 AM, AKSHAY BHAT wrote: > Hi there, > > I was trying to analyse few data sets of A. thaliana through the UCSC > Genome Browser and found that the help menu did not answer many of my > questions. Firstly, the documentation is incomplete on how to add > custom annotation tracks into the browser (only for the A. thaliana > (Arabidopsis thaliana) Genome Browser Gateway). Secondly, I was > wondering on to what specific formats the Genome Browser would > accept A. thaliana data because the Human Genome Browser suggests > bedGraph<http://genome.ucsc.edu/goldenPath/help/bedgraph.html>, > GTF<http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#GTF>, > PSL<http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#PSL>, > BED<http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#BED>, > bigBed<http://genome.ucsc.edu/goldenPath/help/bigBed.html>, > WIG<http://genome.ucsc.edu/goldenPath/help/wiggle.html>, > bigWig<http://genome.ucsc.edu/goldenPath/help/bigWig.html>, > BAM<http://genome.ucsc.edu/goldenPath/help/bam.html>, > VCF<http://genome.ucsc.e! du/goldenPath/help/vcf.html>, > MAF<http://genome.ucsc.edu/goldenPath/help/maf.html>,BED > detail<http://genome.ucsc.edu/FAQ/FAQformat.html#format1.7>, Personal > Genome SNP<http://genome.ucsc.edu/FAQ/FAQformat.html#format10>, and > microarray<http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#microarray> > (BED15). Would it be possible to use these formats for the A. > thaliana Genome Browser. > > Kindly could you clear my questions. I appreciate the concern. > > Best Regards > > Akshay _______________________________________________ Genome > maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
