Dear Hiram and Ewan, thank you for all your help, i found the required info here:
http://www.gramene.org/info/docs/webcode/linking.html Do you plan to enable bigBed/bigWig external data import on Ensembl in the future? best, Gregor On 12/30/2010 7:12 PM, Hiram Clawson wrote: > 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
