Hi Peter, One of our engineers mentioned the BED 4-6 option was added to the multiple option because this was requested by ENCODE users. However for BED12, he says "[looking at the code] if the range find on the chain returns two or more top-scoring chains of the same score, it calls it "duplicated-in-new" and returns without outputting anything else. In theory this could be relaxed so that multiple qualifying chains would be output. Obviously, it might be harder for the user to analyze the results if there are many chains. I suppose a different way would be to let the user choose the topN high-scoring chains as a way to deal with regions with many hundreds or thousands of hits."
Please contact us again at [email protected] if you have any further questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 11/17/2011 6:34 AM, Peter Ebert wrote: > Hi, > liftOver informed me that, when using the -multiple option, it can only use > files in BED4/5/6 format as input. Is that a technical (= programming related) > limitation or is there a more complicated explanation? It would be nice if > someone could elaborate on that issue. > Thanks in advance. > Cheers, > Peter > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
