Bedtools subtract not dealing well with large datasets

Question

[roll]

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

[karl.stamm]

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.

Answer 1

[roll]

bedtools intersect -v