See Standard BED format http://genome.ucsc.edu/FAQ/FAQformat#format1
-bedPlus=N - File is bed N+ format -bedPlus=3 means that only the first 3 columns are treated as a standard BED file. Any columns after 3 are just carried along passively. Since the format of this data is not a BED 6, you either need to try to use -bedPlus=3 because only the first 3 columns match the bed standard, or else re-arranage the columns into a standard BED 6 so that the strand and name information at least could be used. If you need to carry along a second identifier, the user could make it into a bed 6 plus with dummy score column of 0. -Galt On Fri, 21 Aug 2009, Guruprasad Ananda wrote: > Hi, > > I'm Guru from Galaxy team, and one of our users has pointed out an > issue with the liftOver tool which uses your liftOver binary. The > problem seems to be with input datasets containing 6 columns. The > output dataset in such cases will contain the 1st 5 columns intact, > but only the 1st character of the 6th column for some reason. Can you > please explain why this is the case? > I'm pasting sample input and output below for mm9 to hg18 mapping: > Input: > chr3 45665675 49665675 + 3-47575860 abcd > chr3 45665875 49675675 + 4-47575860 abcde > > Output: > chr4 134785199 138758353 + 3-47575860 a > chr4 134785199 138767293 + 4-47575860 a > > Also, I noticed that if I change the -bedPlus option of liftOver > binary to 3 (I'm guessing the default is 6?), it works fine. Could > you please elaborate a little bit about this option? > > Thanks, > Guru. > Galaxy team. > > Guruprasad Ananda > Graduate Student > Bioinformatics and Genomics > The Pennsylvania State University > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
