somehow the Operate On Genomic Intervals - Intersect the intervals of two data sets doesn't work. Data sets which clearly have overlapping intervals (I checked on UCSC browser) return empty intersect files (green, no error message). I generated narrow peak files from peak calling in galaxy and then tried to intersect those: empty files on 3 technical replicates from a published dataset. Then cut just the first 6 columns and converted into bed with defined attributes: still the same.
Can somebody please check what's going on with that tool?
I wanted to use Galaxy for a workshop on ChIP-Seq data analysis, but it seems a bit buggy :/