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
