yeah thanks. i'm using your tRNAs.txt, wgRNA.txt, as well as mirbase and Biomart. seems to be working out OK. although i did like your RNAGene.txt for hg18 which appears to have not been created for hg19. JK
> 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 >> > Jim Kozubek freelance writer and MS student in genetics 10 Kaya Lane Mansfield Center, CT 06250 (603)264-9267 "The universe has no memory" -old proverb, also, in maritime culture, the sea has no memory _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
