Bedtools subtract not dealing well with large datasets
I am using bedtools subtract with large datasets and it keeps crashing, giving the following error
terminate called after throwing an instance of 'std::bad_alloc'
Is there a way to get over this problem in bedtools?
Alternatively is there any other way to find non-overlapping regions for two bed files?
thanks
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Watch the process in another terminal window with "top". std::bad_alloc sounds like a memory error, maybe it used all of your memory then ran out? Pre-sorting both lists might help.