Question: Unable to define a CrisprSet because of missing target location
gravatar for lillyv
2.7 years ago by
lillyv0 wrote:

> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252    LC_MONETARY=German_Germany.1252 LC_NUMERIC=C                   
[5] LC_TIME=German_Germany.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] rtracklayer_1.34.2   CrispRVariants_1.2.0 ggplot2_2.2.1        Rsamtools_1.26.1     Biostrings_2.42.1    XVector_0.14.0      
 [7] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3  IRanges_2.8.1        S4Vectors_0.12.1     BiocGenerics_0.20.0  BiocInstaller_1.24.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.9                plyr_1.8.4                 bitops_1.0-6               tools_3.3.2               
 [5] zlibbioc_1.20.0            digest_0.6.12              RSQLite_1.1-2              memoise_1.0.0             
 [9] tibble_1.2                 gtable_0.2.0               lattice_0.20-34            Matrix_1.2-8              
[13] DBI_0.5-1                  gridExtra_2.2.1            stringr_1.2.0              grid_3.3.2                
[17] Biobase_2.34.0             AnnotationDbi_1.36.2       XML_3.98-1.5               BiocParallel_1.8.1        
[21] reshape2_1.4.2             magrittr_1.5               scales_0.4.1               GenomicAlignments_1.10.0  
[25] assertthat_0.1             SummarizedExperiment_1.4.0 colorspace_1.3-2           stringi_1.1.2             
[29] RCurl_1.95-4.8             lazyeval_0.2.0             munsell_0.4.3

> crispr_set <- readsToTarget(reads = "subsample.bam" , target = gr, reference = reference, target.loc = 200)
Read 694 alignments, excluded 0

0 from 692 (0.00%) chimeras did not involve guide
692 from 692 (100.00%) remaining chimeric reads included
0 (0.00%) assigned to more than one target

0 of 2 nonchimeric reads span the target range

Initialising CrisprRun subsample.bam

Initialising CrisprSet lenti_zeo_self_targeting:4840-5460 with 1 samples
Error in .self$.genomeToTargetLocs(target.loc, start(target), end(target),  : 
  unused argument (rc = rc)


Would someone be so kind to explain to me what this error message means?


ADD COMMENTlink modified 2.7 years ago by helen.lindsay0 • written 2.7 years ago by lillyv0
Answer: Unable to define a CrisprSet because of missing target location
gravatar for helen.lindsay
2.7 years ago by
European Union
helen.lindsay0 wrote:

This is a bug that occurs when all of the reads are mapped as chimeras, sorry!  It's now fixed in devel version 1.3.4.

Best wishes,


ADD COMMENTlink written 2.7 years ago by helen.lindsay0
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