Hi. I want to cluster the 5'cap TSSs of wild-type and mutant strains. In R, I have tried using CAGEr package, but I'm having problems importing bam files and turning them in ctss object with CAGEr.

Here is how my script looks:

library(CAGEr) library(BSgenome.Scerevisiae.UCSC.sacCer3) library(MultiAssayExperiment) library(SummarizedExperiment)

rm(list = ls())

inputFiles = list.files( "../../Macintosh HD/Users/ru84wix/Desktop/mount/5capseq/novoalign/deduplicated/" , "bam$" , full.names = T)

ce <- CAGEexp( genomeName = "BSgenome.Scerevisiae.UCSC.sacCer3" , inputFiles = inputFiles , inputFilesType = "bam" , sampleLabels = sub( "_extracted_deduplicated.bam", "", basename(inputFiles)) )

getCTSS(ce, correctSystematicG = F)

Error in checkSlotAssignment(object, name, value) :

assignment of an object of class “IRanges” is not valid for slot ‘ranges’

in an object of class “UnstitchedGPos”; is(value, "UnstitchedIPos") is not TRUE

How can I solve this problem?