The intersect tool under "Operate on Genomic Intervals" has suddenly disappeared. Is this a bug or was the tool intentionally removed? Either way it's a shame as it was one of the tools I used all the time.
Can anyone suggest a comparable tool for identifying regions in a BED file that overlap with regions in another BED file? It seems to me that the BEDTools "Intersect Multiple Sorted BED Files" might be usable, but it reports a lot of information I don't need or want and makes the task of identifying overlap far more laborious. Thanks!