Hi,

I am generating overlaps using this command in bedtools:

intersectBed -a snps.bed -b region.bed -wb

And now I am trying to compare the same files using the R package GenomicRanges, countOverlaps(snps, region.bed, type=c("within"), but I am not getting the same results. 

In particular, it seems as the positions at the borderline of the region.bed are not counted as overlaps,
for example this entry in snps.bed:
1	112162878	112162879

and this entry in region.bed:
1       112162834       112162878

Is this what others have seen as well? How can I get bedtools to count these entries as overlaps, without adding flanking bases?
Thank you

BED files are generally 0-indexed, so you're generally not going to get overlaps with applications that do operations on input files that use 0-based indexing, which generally do not count endpoints in calling overlaps. GRanges documentation says it uses 1-based indexing, so it will include endpoints in generating overlaps. 

Your solution is perhaps not to count those kinds of overlaps in BED file inputs using GRanges, by specifying that your (BED-formatted) inputs are 0-based and need adjustment in R. The [documentation][1] for GRanges explains this in more detail; see the `starts.in.df.are.0based` option.


  [1]: https://bioconductor.org/packages/3.3/bioc/manuals/GenomicRanges/man/GenomicRanges.pdf