How to use R`s Short read package to get a quality report on a set of paired fastq files?

Question

[human_genomeXXX]

How to use R`s Short read package to get a quality report on a set of paired fastq files?

I run the code: **

**    library("ShortRead")
       fls <- dir("//XDR_MARCH_2016//Pure_FASTQ_Converted//", "*fastq$", full=TRUE)
      qaSummary <- qa(fls, type="fastq")
       browseURL(report(qaSummary))**

**

and get --- Error in slot(object, ".srlist") : cannot get a slot (".srlist") from an object of type "NULL"

How to fix that? Are there alternative R packages for assessment of the quality of WGS short reads?

[Brian Bushnell]

Why not use FastQC? For that matter, BBMap produces a great set of histograms from reads that tell you the actual error rates rather than Illumina's quality scores. For example, add the flags "mhist=mhist.txt qhist=qhist.txt"; then you can plot those files in R/Excel.

[human_genomeXXX]

Thank you, does BBMap able to call FASTQC directly?

[Brian Bushnell]

No, they are independent. But FastQC is very easy to use.

[WouterDeCoster]

Can you check if your variables fls and qaSummary are what you expect them to be? Does fls contain files?