readAndMerge() different outputs everytime I run it

[Former user]

Hi,

First of all thank you very much in advance.

I wanted to merge my biological replicates and I found the readAndMerge(). Therefore, I run the chicagoPipeline as follows:

testDesignDir <- file.path("desingDir/")
# testDataPath <- file.path("chinputs")
# files <- c(
#   file.path(testDataPath, "BR1.chinput"),
#   file.path(testDataPath, "BR2.chinput")
# )
# 
# library(Chicago)
# cd <- setExperiment(designDir = testDesignDir)
# cd <- readAndMerge(files=files, cd=cd)
# cd <- chicagoPipeline(cd)
# outputDirectory <- "merge"
# exportResults(cd, file.path(outputDirectory, "sample"))
# saveRDS(cd, file.path(outputDirectory, "sample.Rds"))
# 

But I have notice that everytime I run this script I obtain a different number of interactions in the seqmonk file. Is that possible?