DONE searching finish off-target search in sequence 2 finish off-target search in sequence 1 finish feature vector building finish score calculation [1] "Done!" Error in $<-.data.frame(*tmp*, "offTarget_Start", value = logical(0)) : replacement has 0 rows, data has 383379 In addition: There were 50 or more warnings (use warnings() to see the first 50)

annotatedOfftargets <- annotateOffTargets(offTargets, + txdb = TxDb.Hsapiens.UCSC.hg38.knownGene, + orgAnn = org.Hs.egSYMBOL) Error in subset(thePeaks, !is.na(offTargetStart) & offTargetStart != : object 'offTargets' not found offTargets Error: object 'offTargets' not found

Hi Tom,

I tried to run the analysis with a smaller input bed file, and did not get the same error. I am wondering whether the error is from running the analysis with the entire dataset or just chr6 you shared with me.

Thanks!

Best, Julie

Hi Tom,

I tried to run the analysis with a smaller input bed file, and did not get the same error. I am wondering whether the error is from running the analysis with the entire dataset or just chr6 you shared with me.

Thanks!

Best, Julie

Hi Tom,

Please add strand information to the peak bed file that should resolve the issue.

offTargetAnalysisOfPeakRegions was internally called by GUIDEseqAnalysis which generates strand information automatically.

You made me realize that the function offTargetAnalysisOfPeakRegions could be very useful if you already have a list of peaks at hand.

I will modify the script by adding + to the strand column if the input peak bed file only contains 3-5 columns, and adding a name column if the input peak bed file only contains 3 columns.

Thanks!

Best, Julie

Hi Tom,

The 5th column stores score, which should be numeric. Therefore, it should only contain numbers.

FYI, I have modified the script which is able to handle peak bed files with 3 or more columns. Please download the updated version GUIDEseq 1.7.1 using git clone git@git.bioconductor.org:packages/GUIDEseq).

Best, Julie