I have built a custom BSgenome package for an in house assembly of my organism's genome. I am receiving a "UCSC library operation failed" when I attempt to use the seqinfo(BSgenome) as the genome parameter for the quantifyCTSSs function of CAGEfightR. I have looked through the code underlying the CAGEfightR package (https://github.com/MalteThodberg/CAGEfightR) but cannot locate where it makes a call to the UCSC library. Can anyone help explain?
Please note: As I do not have ownership of some of the underlying data, I am limited to what I can post.
CTSSs <- quantifyCTSSs(plusStrand = bw_plus, minusStrand = bw_minus, genome = seqinfo(BSgenome), design = CAGEtable)