How to use R`s Short read package to get a quality report on a set of paired fastq files?
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?
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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.
Thank you, does BBMap able to call FASTQC directly?
No, they are independent. But FastQC is very easy to use.
Can you check if your variables
flsandqaSummaryare what you expect them to be? Doesflscontain files?