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
