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
