My ATAC-seq samples have both pair-end 50 and pair-end 100 reads. After peak calling using macs2, can I directly compare the counts of the regions defined by these peaks from different read lengths?

library(Rsubread)
library(GenomicRanges)
library(DESeq2)

peaks <- dir("peaks/", pattern = "*.narrowPeak", 
             full.names = TRUE)

myPeaks <- lapply(peaks, ChIPQC:::GetGRanges, simple = TRUE)

myGRangesList<-GRangesList(myPeaks)   
reduced <- reduce(unlist(myGRangesList))
consensusIDs <- paste0("consensus_", seq(1, length(reduced)))
mcols(reduced) <- do.call(cbind, lapply(myGRangesList, function(x) (reduced %over% x) + 0))
reducedConsensus <- reduced
mcols(reducedConsensus) <- cbind(as.data.frame(mcols(reducedConsensus)), consensusIDs)

bamsToCount <- dir("bam/", full.names = TRUE, pattern = "*.\\.bam$")


regionsToCount <- data.frame(GeneID = paste("ID", seqnames(reducedConsensus), 
                                            start(reducedConsensus), end(reducedConsensus), sep = "_"), Chr = seqnames(reducedConsensus), 
                             Start = start(reducedConsensus), End = end(reducedConsensus), Strand = strand(reducedConsensus))


fcResults <- featureCounts(bamsToCount, annot.ext = regionsToCount, isPairedEnd = TRUE, 
                           countMultiMappingReads = FALSE, maxFragLength=1000)

myCounts <- fcResults$counts

colnames(myCounts) <- c("sample_1", "sample_2", "sample_3", "sample_4")



# [generate the metadata] to describe/group the samples
Group <- factor(c("Control", "Control", "Treat","Treat"))

metaData <- data.frame(Group, row.names = colnames(myCounts))
atacDDS <- DESeqDataSetFromMatrix(myCounts, metaData, ~Group, rowRanges = reducedConsensus)
atacDDS <- DESeq(atacDDS)

atac_Rlog <- rlog(atacDDS)

rawCounts <- counts(atacDDS, normalized = FALSE)

Thanks