Hi Lei, Thank you for bringing this to our attention. We checked with the authors of RepeatMasker and found out the following information:
"The "?" is a statement about the confidence of the classification call. When a curator comes across a new repeat they often are unsure of it's type. It may look like a DNA transposon but it's method of duplication is not verified. So the curator will tentatively put it into the DNA Transposon class as a "DNA?/..." At some point in the future either the "?" will be removed or the classification will be changed." We have changed the way repeats with a "?" in their class are displayed in the browser. Before, they were displaying in "Other," but we've changed it so they display with the group the curator suspects they belong to. For example, those with a class of DNA?, will now display with the DNA repeats in the browser. This change won't be on our public site for another few weeks, but you can see it on our genome-test site now: genome-test.cse.ucsc.edu. Because much of data the on genome-test that has not yet been through quality review, please use discretion when downloading and viewing data from genome-test as it may still be undergoing changes and improvements. Please contact the mail list ([email protected]) again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group On 10/28/11 3:17 AM, Gu, Lei wrote: > Dear UCSC genome browser, > > Would you please tell me what's the meaning of the question mark for some > repFamily and Class in the rmsk table? > Thanks! > > Best, > Lei > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
