Hi, Assif! Presently there is no support in the browser for type=bigBedDetail. Perhaps we'll be able to add it at some point.
Meanwhile, I see that you are using spaces in your names in the ones with /// characters. The slash chars themselves are OK. Because the BED format is officially white-space separated this means that you should not use any white-space within the name field (or any other field). It also means you should not have an empty field such as your field 14 presently is, since multiple whitespace chars act as a single separator. As it is, I can get your data to make a bigBed with this command: bedToBigBed -type=bed12+1 test_bb.BED /cluster/data/hg19/chrom.sizes test.bb if I remove the space in the name field. If you populate that 14th column with actual values then this command should work: bedToBigBed -type=bed12+2 test_bb.BED /cluster/data/hg19/chrom.sizes test.bb -Galt On Tue, Jul 10, 2012 at 8:32 AM, Assif Yitzhaky < [email protected]> wrote: > Dear supporter, > > > 1. I would like to ask whether the BED detail format (which includes > 2 additional columns) can be transformed into the bigBED format? When I try > to transform BED detail format to bigBED using the function bedToBigBed it > fails. > > I get this error: > > ./bedToBigBed test_bb.BED hg19.chrom.sizes test.bb > pass1 - making usageList (1 chroms): 1 millis > Error line 1 of test_bb.BED: expecting 187185 elements in expIds list (bed > field 14) > > > 2. In the regular BED format, it seems that "///" (slashes) are > forbidden in the 4 column (name) if one would like to transform such file > into bigBed format. > > For example, I get this error: > > > > ./bedToBigBed test_bb_no_details.BED hg19.chrom.sizes test.bb > > pass1 - making usageList (1 chroms): 1 millis > > Expecting 12 words line 514 of test_bb_no_details.BED got 14 > > > > An example of an input of BED detail format for the bedToBigBed function > (the 14th column is empty, but it fails also if it is not) can be > downloaded from: > > > > > http://www.weizmann.ac.il/complex/compphys/software/Amit/primers/human/tmp/test_bb.BED > > > > When discarding the 13th and 14th columns so that the file is a regular > BED file and removing lines with /// (slashes), the function bedToBigBed > seems to work fine. > > > > > > Thanks a lot, > > > > Assif Yitzhaky > > Weizmann Institute of Science > > > > > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
