At the moment, BSFind uses two parameters, merge.minCrosslinks and merge.minClSites which are a bit hard to distinguish. merge.minClSites refers to the pureclip sites and merge.minCrosslinks to the crosslinked nucleotides.
Maybe we could rename them for clarity:
merge.minClSites could become merge.minCalledSites
merge.minCrosslinks could become merge.minCrosslinkedSites
The description of the parameters could also be altered:
merge.minCalledSites
the minimal number of sites from peak calling (e.g. pureclip sites) that have to overlap with the final binding sites
merge.minCrosslinkedSites
the minimal number of crosslink sites (meaning crosslinked nucleotide positions) that have to overlap a final binding site
At the moment, BSFind uses two parameters,
merge.minCrosslinksandmerge.minClSiteswhich are a bit hard to distinguish.merge.minClSitesrefers to the pureclip sites andmerge.minCrosslinksto the crosslinked nucleotides.Maybe we could rename them for clarity:
merge.minClSitescould becomemerge.minCalledSitesmerge.minCrosslinkscould becomemerge.minCrosslinkedSitesThe description of the parameters could also be altered:
merge.minCalledSitesthe minimal number of sites from peak calling (e.g. pureclip sites) that have to overlap with the final binding sites
merge.minCrosslinkedSitesthe minimal number of crosslink sites (meaning crosslinked nucleotide positions) that have to overlap a final binding site