bedtools closest gives a -1 distance with -io (ignore overlaps)
I am using bedtools closest to find the closest feature to my peaks. I used unix sorted files (sort -k1,1 -k2,2n a.bed) my command line is
bedtools closest -io -d -sorted -a a.bed -b b.bed
This results in some features in a.bed to have -1 (no other negative value, only -1) distance. Since I asked to ignore overlaps (-io), how does this come about? what does it mean?
many thanks...
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Could this be the reason ?. Help message output from bedtools closest -
Notes: Reports "none" for chrom and "-1" for all other fields when a feature is not found in B on the same chromosome as the feature in A. E.g. none -1 -1