Hi Luvina, thank you very much for the detailed information on liftOver. Regarding the multiple option, I noticed the following: I try to lift BED files of the following format between assemblies: <chr> <start> <end> <name> <dataValue> The output of liftOver is a BED file as follows: <chr> <start> <end> <name> <multiplicity> So, liftOver discards the data value in column 5 and replaces it with the value of the multiplicity for the mapped region (i.e. 1, 2, 3, 4 and so on for multiple output regions). Is it possible to set a liftOver parameter in order to get a file like <chr> <start> <end> <name> <dataValue> <multiplicity> Since this is still a 6 column BED file, it should not interfere with the restrictions of the multiple option? Thanks for your help.
Best, Peter On Tuesday 29 November 2011 20:49:49 Luvina Guruvadoo wrote: > 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
