Good Morning Gregor: For your one-click operation, please use the bigBed/bigWig data types in your URL specification. http://genome.ucsc.edu/goldenPath/help/bigBed.html http://genome.ucsc.edu/goldenPath/help/bigWig.html
These types of URLs are much more efficient than ordinary URLs to data files that have to be completely fetched over the Internet each and every time they are used in your one-click operation. bigBed/bigWig data URLs do not transfer the entire file, and any bits of the file that are transferred are temporarily cached at UCSC and re-used by any subsequence access from other users of your application without any additional transfer of data. As Ewan mentions, you can use a URL to submit data to Ensembl: http://www.ensembl.org/info/website/upload/index.html However, I do not notice an option there to use bigBed/bigWig data types with the advantage of the cached bits of file transfer. --Hiram Gregor Rot wrote: > Dear Ewan, > > thank you for your reply. One more question: the UCSC genome browser has > a very useful feature: to download track data simply by providing a URL, > e.g.: > > http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hgt.customText=http://URL_OF_BED_FILE.gz > > > > (loads the file from the given URL and displays the track in the > browser, in this case for hg19). > > Does Ensembl genome browser support something similar? > > We are building a pipeline and would like to display new tracks in the > browser with one click (simply opening a URL in a new browser window). > > thank you, > best regards, > Gregor > > On 12/28/2010 8:32 PM, Ewan Birney wrote: >> >> Gregor: >> >> The Dictyostelium discoideum genome is in the Ensembl Genomes >> project (sister project to Ensembl, using the same software) >> at: >> >> http://protists.ensembl.org/Dictyostelium_discoideum/Info/Index >> >> >> Ensembl Genomes Release 7 supports many of the common user upload >> formats, including indexed BAM files and the well used UCSC formats, >> such as bed, wig and bedgraph. I've blogged about this recently >> at: >> >> http://ensembl.blogspot.com/2010/12/beds-wigs-bams-and-variants-for-flies.html >> >> >> >> >> >> We don't have Dictyostelium purpureum but it is in scope to add; we'd be >> aiming to work with the Dicty community if we were to. >> >> >> >> Ewan Birney >> >> >> >> >> On 28 Dec 2010, at 19:11, Hiram Clawson wrote: >> >>> Good Morning Gregor: >>> >>> Please note this discussion: >>> >>> http://genomewiki.ucsc.edu/index.php/How_to_submit_a_new_genome >>> >>> Please note, our focus here at UCSC is on vertebrate genomes. >>> We do not display amoeba genomes. You could install a local >>> copy of the genome browser to host these genomes at your >>> institution. >>> >>> --Hiram >>> >>>> Dear UCSC team! >>>> >>>> Congratulations on the great work in building the genome browser. >>>> >>>> I am wondering if there is a way to add a new genome to your browser, i >>>> would like to add 2 genomes: >>>> >>>> Dictyostelium discoideum >>>> Dictyostelium purpureum >>>> >>>> The assembly and annotation are both available from >>>> http://dictybase.org >>>> >>>> Thank you & best regards, >>>> Gregor >>>> >>>> ---------- >>>> Gregor Rot >>>> http://www.fri.uni-lj.si/en/gregor-rot >>>> Bioinformatics Laboratory >>>> Faculty of Computer and Information Science >>>> Trzaska 25 >>>> 1000 Ljubljana >>>> Slovenia _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
