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?
• 2,782 views
•
link
written
by
human_genomeXXX •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when run SamToFastq
written by Lila M
-
Error during demultiplexing by bcl2fastq
written by daffodil •
-
Monocle3 cell data set object (grabbing values from one column)
written by seattlescientist_01 •
-
How to set (or change) values in minfi::‘RGChannelSet’ object
written by Bosberg •
-
bumphunter for 3 (or more) groups
written by alfonsosaera •
-
Using snpStats to read a pedfile, object 'm' not found
written by nadrianam •
-
Tutorial: InsideDNA: Improving quality of raw fastq data with Trimmomatic and RemoveBadTiles
written by shilparaopradeep •
-
How to write a i in loop for readfastq function
written by Reprogrammer •
-
GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
written by user31888
-
Tool: ChIPQC: a package for assessing quality of ChIP-seq samples and experiments
written by Rory Stark
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?