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Question: Error with qa() in package ShortRead when checking for adapter contamination.
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gravatar for Diego Diez
2.5 years ago by
Diego Diez730
Japan
Diego Diez730 wrote:

I am trying to get a report on some NGS data and estimate adapter contamination. This code works without problem:

library(ShortRead)
## ff is a vector of fastq files.
qa <- qa(ff, type = "fastq")

The following code, however, ends with an error message:

qa <- qa(ff, type = "fastq", Lpattern = "AATGATACGGCGACCACCGAGATCTACACTCGTCGGCAGCGTCAGATGTG")
Error in slot(object, ".srlist") : 
  cannot get a slot (".srlist") from an object of type "list"

I tried inputing the sequence as a AAString object without success:

qa <- qa(ff, type = "fastq", Lpattern = AAString("AATGATACGGCGACCACCGAGATCTACACTCGTCGGCAGCGTCAGATGTG"))

Am I doing something wrong? What would be the proper way to perform this analysis?

> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.3 (El Capitan)

locale:
[1] C/UTF-8/C/C/C/C

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

other attached packages:
 [1] ShortRead_1.28.0           GenomicAlignments_1.6.3   
 [3] SummarizedExperiment_1.0.2 Biobase_2.30.0            
 [5] Rsamtools_1.22.0           GenomicRanges_1.22.4      
 [7] GenomeInfoDb_1.6.3         Biostrings_2.38.4         
 [9] XVector_0.10.0             IRanges_2.4.7             
[11] S4Vectors_0.8.11           BiocParallel_1.4.3        
[13] BiocGenerics_0.16.1       

loaded via a namespace (and not attached):
 [1] lattice_0.20-33      bitops_1.0-6         grid_3.2.3          
 [4] futile.options_1.0.0 zlibbioc_1.16.0      hwriter_1.3.2       
 [7] latticeExtra_0.6-28  futile.logger_1.4.1  RColorBrewer_1.1-2  
[10] lambda.r_1.1.7      
ADD COMMENTlink written 2.5 years ago by Diego Diez730
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