Hi Anjuska, Sorry for the delayed reply...
One of our engineers had these comments: " In the snoMiRna (a.k.a. wgRna) table, we have some pre-miRNAs (don't be confused by the fact that the type column says that they're miRNAs. miRNAs are actually the mature miRNAs chopped out of pre-miRNAs, and are approximately 22 nucleotides in length. The 'miRNAs' in the wgRna table are 138 nts in length). FWIW, this table is a few years old now. Given the rate at which miRNA data is accumulating, that makes it "old". To my knowledge, we don't have any tracks of mature miRNAs. There are also /some/ pre-miRNAs in UCSC Genes, via Rfam. The way to spot them is that in the kgXref table, rfamAcc is not "" and geneSymbol matches 'Mir*'. So unfortunately, we don't have a direct way to distinguish 3' and 5' miRNAs. The best we can do is the pre-miRNAs that they came from. Alternatively, the user could download the miRNA coordinate data from miRBase ( http://www.mirbase.org/ftp.shtml) and load it as a custom track. The coordinates are in GFF3 format, so we should be able to read them. The miRBase coordinate data contains both pre-miRNAs and mature miRNAs, but they're easily distinguished by the contents of the type field." Please let us know if you have any additional questions or need help with anything suggested above: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 5/5/12 3:49 PM, Anjuska Kyllönen wrote: > Hello, > > I can find only one table (sno/miRNA) for microRNAs and I have used it > for looking at miRNA expression in my NGS data. However for my > research it is critical to get the expression differences between 5p > and 3p miRNAs. What table should I use? > > Thank you in advance, > Anjuska Kyllönen > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
