Entering edit mode
8.4 years ago
tako
•
0
I am analyzing two different datasets using bedtools intersect, and would like to see how closely they match by running bedtools intersect. From the documentation provided online, I can see that the "-r" option would filter for reciprocal overlaps of any given fraction using "-f". To me, this sounds like running both "-f" and "-F" at the same time. However, I get vastly different results when running "-f 0.5 -r" and running "-f 0.5 -F 0.5". Can anybody explain the difference?
To give more details, the option "-f 0.5 -r" gives thousands of results, while "-f 0.5 -F 0.5" only gives a dozen or so results.
-f 0.5 -r
is same as-f 0.5 -F 0.5
but if you want to specify a different overlap threshold from two features, you could now use-f 0.5 -F 0.7
which was not possible with-r
.-r
just uses the same fraction of overlap as that of-f
for file B, but now you could specify a different reciprocal fractions using-F
Hope I did not confuse you more.
If you see a difference, it would be good if you post an example, helps to troubleshoot.
Added more info. The results are not the same.
you need to post an example. May be the lines that differ from -f -r Vs -f -F
Mmmm.. I wouldn't risk my neck for what I am going to say but, are you getting more overlaps when you specify
-f 0.5 -F 0.5
? One reason that springs into my mind is that -f 0.5 -F 0.5 arguments is set, maybe A fulfils the condition, but B does not, and the record is printed. While if "-f 0.5 -r" is set, both A and B must met the condition to be printed.Anyway, the best way to address the problem is to create a test data and try to check it yourself :)
I'm actually getting far less results for -f 0.5 -F 0.5