I am a new post-doc at Washington State University. I don’t have a whole lot of bioinformatics experience, nevertheless I am trying to use CRISPRseek on the Arabidopsis genome.
Using a small test set (two genes), I can identify gRNA candidates, but there is a problem with the OfftargetAnalysis.xls in that the exon location is not being annotated and neither is the gene id.
What mistake am I making?
> outputDir <- getwd()
> inputFilePath <- system.file('extdata', 'TAIR10_cds_20110103_representative_gene_model_updated.fa', package = 'CRISPRseek')
> REpatternFile <- system.file('extdata', 'NEBenzymes.fa', package = 'CRISPRseek')
> results <- offTargetAnalysis(inputFilePath, findgRNAsWithREcutOnly = FALSE, REpatternFile = REpatternFile, findPairedgRNAOnly = FALSE, BSgenomeName = Athaliana, chromToSearch = "all", txdb = TxDb.Athaliana.BioMart.plantsmart22, orgAnn = org.At.tair.db, max.mismatch = 4, outputDir = outputDir, overwrite = TRUE)
The main thing I want to see is whether the off-target is exonic and the Arabidopsis locus ID (i.e. something looking like AT1G11110) for each off-target hit.
Thank you for any insight you can give me.