Entering edit mode
7.1 years ago
xiaoyonf
▴
60
Hello,
May I get clear explanation of the difference of command "-wa" and "-u" in the "intersect" tool of bedtools? In order to get an overlap between two gene intervals, I once used the "-wa" to get common set of A and B, and "-v" to get unique set in A vs B. But I found that the total number of intervals of unique and common is not equal to the whole set of "A", after using "-wa" and "-v". But the "-u" seems work to pull out the common set without the issue. Thanks, Xiaoyong
I now figured out that "-wa" will report all the intervals in "A" overlapping with one or more intervals in "B". If one interval in A overlaps with >1 intervals, under "-wa", it will still report >1 times in the output, thus making the replicates. "-u" will report only once even there are >1 overlaps. Thanks, Xiaoyong