HI,
I am new to bed file manipulations. I have two bed files like follows:
A.BED
Chr1 90 111
Chr1 95 110
Chr1 102 115
Chr1 105 118
Chr1 107 119
Chr1 117 130
B.BED
Chr1 100 120
Now I would like to retain reads that is outside the range of B.BED. I mean I would like get the following as output
Chr1 90 111
Chr1 95 110
Chr1 117 130
How can I get the above following output using bedtools or bedops. Kindly guide me
•
written
by
EVR
2 answers
Via bedops, you can get all elements from set A which do not overlap entirely in set B via the -n 100% option:
$ bedops -n 100% A.bed B.bed > answer.bed
$ more answer.bed
Chr1 90 111
Chr1 95 110
Chr1 117 130
Basically, if there is any portion of an interval in A that is outside of B, -n 100% will report that interval.
It is the converse operation of -e 100%, if that helps. The -e 100% option reports all elements in A that are contained fully within elements in B, and, accordingly, -n 100% reports all elements which are not.
For details, please see: https://bedops.readthedocs.io/en/latest/content/reference/set-operations/bedops.html#not-element-of-n-not-element-of
bedtools intersect -v -a <A.BED> -b <B.BED>
for more instruction read this: http://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
-v option -> Only report those entries in A that have no overlap in B!
This can easily be done in AWK!
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