I am trying to annotate my integration file with the nearest gene names and distance to the nearest gene (upstream and downstream) using hiAnnotator [nearestGenes <- getNearestFeature(alldata.rd, genes.rd ,"NearestGene")].
In the annotation file i could get the the nearest gene name and the distance to my integration, but i assume the distance is calculated from the midpoint of the gene coordinates (start+stop/2).
If i look at the output file, for the insertion Ins1 at Chr10:75097800, which is actually present with in the boundary of Bcr gene, the distance to the gene is showing 36905 [expected output is Dist 0]. Is there any way by which we can get the distance taking boundary into consideration?
gene reference file