Hey Jim, You're correct that the annotated RNA element types are spread out through several different databases. On top of this, there are many species of RNA that are poorly understood and thus poorly annotated. The ENCODE project, for which UCSC serves as the Data Coordination Center, is attempting to shed some light on this problem, but it is early days yet.
If you want to get an idea of the variation that appears in RNA-seq data sets with libraries built from different cell types, and from different cellular compartments, you might want to check out the RNA-seq tracks on our preview browser. http://genome-preview.cse.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRnaSeqSuper This is a link to our preview browser where the data has not yet been through our QA process. I hope this answers your question. If you have any follow-up questions, please respond to this list. Brian On Wed, Mar 16, 2011 at 4:42 PM, Jim Kozubek <[email protected]> wrote: > I wrote a perl script to check all of our Tophat output against RNAgene > (to determine our distribution of "RNA biotypes," such as tRNA, rRNA, > miRNA... etc) but i get the impression that the RNAgene track is not > comprehensive in itself. it seems like a researcher needs to consult 4 or > 5 databases/tracks to get a full understanding of the RNA distribution in > their seq data? in other words, RNAgene includes snoRNA but i suppose it > does not include all of the known snoRNA, otherwise their wouldn't be a > separate track for snoRNA. Thus if I have RNA seq and want to understand a > distribution of biotypes, it seems like i would have to consult > independent databases on rnaGene, refFlat, snoRNA, mirbase... etc etc..? > > > > Jim Kozubek > freelance writer and MS student in genetics > 10 Kaya Lane > Mansfield Center, CT > 06250 (603)264-9267 > > "What can be shown, cannot be said" > L. Wittgenstein > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
