It depends on what you mean by "strand-aware". Currently,
csaw is slightly strand-aware in that directional read extension behaves differently for reads mapped to different strands. Other than that, though, there's not much distinction made between strands.
I've have to know more about the nature of the strand specificity in your experiment, in order to give some better advice. I don't think I've ever dealt with strand-specific IP's before, given that the pulled-down DNA is double-stranded to start with (unless you've got stuff like ChIP-Exo data).
Edit: Given that strand-specific counting seems to be pretty useful, I've added a
forward option to the
readParam object. This'll tell
regionCounts) whether or not to extract and count reads on the forward, reverse or both strands.
I've also added a
strandedCounts wrapper function to easily get both forward- and reverse-strand counts for genomic bins or regions. Word of warning, though; the downstream functions in
csaw that work with
GRanges are not designed to be strand-aware, so some extra work will be necessary if you want, e.g., sensible strand-specific clustering. Check out
?strandedCounts for examples.
These updates should be active in the 1.1.19 build on BioC-devel; give it a day or so to go through.