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
