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 :/
Are you working at http://usegalaxy.org or can you reproduce the problem there? If so, we'd like to review the inputs and tool to find out what exactly is going on. This is how to send in a bug report: https://galaxyproject.org/issues/#usage-problem-reporting
Please include a link to this post in the comments of the bug report.
Thanks! Jen, Galaxy team
Yes, I work on main. Have a look at parallel thread on GitHub: https://github.com/galaxyproject/galaxy/issues/3905#issuecomment-292720519
Have a look at my history https://usegalaxy.org/u/atvb2017/h/unnamed-history
Perfect, reviewing now