Hi Julie,

Given the below input, GUIDEseqAnalysis(outputDir) only stores "PlusMinusPeaksMerged.xls" and "offTargetsInPeakRegions.xls" in the specified directory. "#name#bamReadSummary.xls" and "#name#PlusMinusPeaksMerged.bed" are stored in the working directory. Is this intentional?

guideSeqResults <- GUIDEseqAnalysis(alignment.inputfile = c("Sc-STS3.bam","negSc-STS3.bam"), umi.inputfile=c("UMIs.txt","UMIs.txt"), gRNA.file = "guiderun1.fa", max.mismatch = 10, BSgenomeName = Hsapiens,txdb = TxDb.Hsapiens.UCSC.hg38.knownGene,orgAnn = org.Hs.egSYMBOL, outputDir="Sc-STS3",n.cores.max = 5)

Thanks,

Tomás

Hi Tom,

It’s intentional. The files in the working directory are for debugging.

Best regards,

Julie

.xls" and "#