I have been using CRISPRseek for a while now, and it has been incredibly useful for my research.
However, an error has been coming up recently for some of my query searches (looking for off-target effects of gRNA templates). When using the following input:
offTargetAnalysis(inputFilePath = input_path, findgRNAsWithREcutOnly = FALSE, REpatternFile = REpatternFile, findPairedgRNAOnly = FALSE, findgRNAs = FALSE, BSgenomeName = Hsapiens, txd = TxDb.Hsapiens.UCSC.hg19.knownGene, orgAnn = org.Hs.egSYMBOL, max.mismatch = 4, scoring.method = "CFDscore", outputDir = output_dir, overwrite = TRUE)
Some of my queries generate the following output:
>>> Finding all hits in sequence chrUn_gl000249 ... >>> DONE searching Building feature vectors for scoring ... Calculating scores ... ERROR : replacement has X rows, data has Y
where X < Y.
Here is the output of sessionInfo():
> sessionInfo(package = 'CRISPRseek') R version 3.4.3 (2017-11-30) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.3 LTS Matrix products: default BLAS: /usr/lib/libblas/libblas.so.3.6.0 LAPACK: /usr/lib/lapack/liblapack.so.3.6.0 locale:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C  LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8  LC_PAPER=en_US.UTF-8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: character(0) other attached packages:  CRISPRseek_1.18.0 loaded via a namespace (and not attached):  compiler_3.4.3 graphics_3.4.3 utils_3.4.3 grDevices_3.4.3  stats_3.4.3 datasets_3.4.3 methods_3.4.3 base_3.4.3