I am using offTargetAnalysis function with CFD scoring method (CRISPRseek verison 1.16.0 from bioconductor) to select a few best-scoring gRNAs for each of a large set of sequences. In the past, I have used the combination of gRNAefficacy and top10OfftargetTotalScore in the summary file as criteria for selection. I wonder whether there are updated version of CRISPRseek that provides a single score that combine the gRNA efficacy and the off-target scores for each gRNA.
On another note, in several recent jobs, I set annotateExon = TRUE, but I did not see any notation in either the "inExon" or the "inIntron" column in the OfftargetAnalysis.xls file. Did I miss something? The script I used is copied below:
results=offTargetAnalysis("exon.fasta", findgRNAsWithREcutOnly = FALSE, annotateExon = TRUE, findPairedgRNAOnly = FALSE, exportAllgRNAs="fasta", txdb= txdb, max.mismatch = 3, BSgenomeName = ss, outputDir = ".", overwrite = TRUE, scoring.method="CFDscore")
Thank you very much for your help!