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jacob.bradford
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@jacobbradford-16692
Last seen 6.2 years ago
Hi,
As part of my research, I am required to run CRISPRseek, however, I am facing issues using the offTargetAnalysis function. I have read the reference manual and found that this function is perfect to help with what I am trying to achieve.
I have pasted my script, input file and the output below.
I run the following script:
#!/usr/bin/env Rscript
library(CRISPRseek)
options(error=function()traceback(2))
library("BSgenome.Mmusculus.UCSC.mm10")
results <- offTargetAnalysis("/home/jake/genomes/mm10-ucsc-mod/chr19/100k/chr19.fa", annotatePaired = FALSE, enable.multicore = TRUE, annotateExon = FALSE, max.mismatch = 3, BSgenomeName = BSgenome.Mmusculus.UCSC.mm10, outputDir = "/home/jake/tools/CRISPRseek/0002", overwrite = TRUE, topN=100000000, chromToExclude="", chromToSearch="ucsc-mm10-chr19-full-extract[10000000-10100000]", findgRNAs=TRUE)
The input fasta file is as follows (/home/jake/genomes/mm10-ucsc-mod/chr19/100k/chr19.fa):
>ucsc-mm10-chr19-full-extract[10000000-10100000] TAATGTACAGCTGGACCGAGAATCTCTGTGGGCTCCTACCTGTTTCTCCTCTTTTCTTCAATACATACTGACCTTCACAAGAGAGCTTGCTATCTAATAGGTGTTCTCTCTCTCTCTCTCTCTCT... (100k bases on a single line)
However, I receive the following error message:
Error in buildFeatureVectorForScoring(hits = hits, canonical.PAM = PAM, :
Empty hits!
Calls: offTargetAnalysis -> buildFeatureVectorForScoring
In addition: Warning message:
In searchHits(gRNAs = gRNAs, PAM = PAM.pattern, BSgenomeName = BSgenomeName, :
No matching found, please check your input sequence, and make
sure you are using the right genome. You can also alter your
search criteria such as increasing max.mismatch!
As according to the error message, I have increased max.mismatch, however, continue to receive the same error.
Could you please help me resolve this?
Kind regards,
Jake.
