Question: Unable to define a CrisprSet because of missing target location
0
gravatar for lillyv
2.5 years ago by
lillyv0
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)

locale:
[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 2.5 years ago by helen.lindsay0 • written 2.5 years ago by lillyv0
Answer: Unable to define a CrisprSet because of missing target location
0
gravatar for helen.lindsay
2.5 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,

Helen

ADD COMMENTlink written 2.5 years ago by helen.lindsay0
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