Small clarification: The plan for now is to continue to include/support the xenoEst/mRna track for primary human genomic going forward. Others will be dropped (or never created) when space becomes an issue.
We hope all this helps, Jennifer Jennifer Jackson wrote: > Hello Shifra, > > We agree with you that the display could be improved for native EST/mRNA > tracks and are discussing options internally but cannot comment yet > if/when a change would be made. Feel free to check back in a month or so > for an update if you do not notice a change before then. > > For the xenoEST tracks, the data has just become too large for us to > support any longer, even as a table/file in the Table browser or on > Downloads. > > One work around is to locate the genomic region(s) in the other genomes > (using the liftOver tool) based on data from the Chain track or using > the Table browser to interpret MAF data from the Conservation track. > Then, use those coordinates to extract EST sequences from the other > genome. Use BLAT to align to the starting genome and upload the results > as a custom track. Obviously, this will be easier and more meaningful if > the genomic regions are shorter and the genomes are phylogenetically > more related or at least limited to a smaller set (rather than the > complete genomic and all possible "other" genomes). > > A second work around would be to use "liftOver" to convert a previously > published xenoEst track to the newer version of genomic (same species > lift) and load results directly (for the web version) or upload as a > Custom track (for the line-command version). Again, this would work best > for smaller regions rather than the entire genome, as the results will > be too large to load as a Custom track. > > Use the Sessions feature to keep Custom track data around longer than 48 > hours (but please remember to keep backups!): > http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Sessions > > Link to web version of liftOver, with instructions for using > line-command liftOver at bottom of page: > http://genome.ucsc.edu/cgi-bin/hgLiftOver > > We appreciate your comments, > Thank you, > Jennifer Jackson > UCSC Genome Bioinformatics Group > > > > shifra wrote: > >> Hi Browser Team, >> >> A development request, if possible. >> >> There are times when there are too many items in a given track to see, >> and it gets compressed into one bottom line. This particularly >> happens in the EST tracks, but also sometimes in mRNAs. When there is >> sequence in all of them, fine, they are usually qualitatively the >> same, and if I can't see all of them, its ok, if I really need them, I >> can get them through the table browser. >> >> But there are instances, like in hg18 chr2:136,591,780-136,591,840 >> (only 61 bp!) there are too many "other ESTs", but the only ones shown >> in the browser are ones without sequence in that area - I just get >> lots of lines going through, when I can't even get the accession >> numbers of the ones I'm interested in! (which are all compressed at >> the bottom). If I go to the table browser, I get all the ESTs, >> because they all go through the area, when I'm only interested in the >> ones with actual sequence in that area. >> >> Is there some way you could program it that when there are too many, >> the ones with sequence in the given area get priority to be shown? >> This happens often actually, I just finally remembered to save a >> specific example... >> >> Another question, I've run into the problem of not having xenoESTs in >> browsers other than human more and more recently. Its a very useful >> track, particularly for other organisms, (like fish for example), when >> several of our scientists would like to compare EST collections of >> species without genomes to species that have sequenced genomes. I >> know that the track did exist in the past, and at some point (if I >> recall correctly) it was removed. Is there any way to consider >> bringing it back? Even if just in table form, and not on the browser? >> >> Thanks, >> >> Shifra >> >> Shifra Ben-Dor, PhD >> Bioinformatics and Biological Computing Unit >> Weizmann Institute of Science >> Rehovot 76100 Israel >> >> [email protected] >> >> tel: 972-8-934-2470 >> fax: 972-8-934-6006 >> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> >> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
