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:  C/UTF-8/C/C/C/C attached base packages:  stats4 parallel stats graphics grDevices utils datasets  methods base other attached packages:  ShortRead_1.28.0 GenomicAlignments_1.6.3  SummarizedExperiment_1.0.2 Biobase_2.30.0  Rsamtools_1.22.0 GenomicRanges_1.22.4  GenomeInfoDb_1.6.3 Biostrings_2.38.4  XVector_0.10.0 IRanges_2.4.7  S4Vectors_0.8.11 BiocParallel_1.4.3  BiocGenerics_0.16.1 loaded via a namespace (and not attached):  lattice_0.20-33 bitops_1.0-6 grid_3.2.3  futile.options_1.0.0 zlibbioc_1.16.0 hwriter_1.3.2  latticeExtra_0.6-28 futile.logger_1.4.1 RColorBrewer_1.1-2  lambda.r_1.1.7