I'm trying to check the quality of my paired end read sequencing data. I am following this pipeline (https://f1000research.com/articles/4-1062#ref-21) which uses QuasR in the first step.

My list of paired files is stored in sampleFile. Currently this file cannot be read into the function. Not sure why. I'm using R studio on a windows operating system.

Also open to using other alignment or QC pathways if I can align to multiple different genomes.

auxFile <- "Ref_Genomes/auxiliaries.txt"
sampleFile <- "./HCV_rna_paired.txt"
genomeName <- "BSgenome.Hsapiens.UCSC.hg38"
td <- tempdir()
proj1<- qAlign(sampleFile, genome=genomeName, auxiliaryFile=auxFile)

Error: cannot open ./HCV_rna_paired.txt

  • 3
    $\begingroup$ Does the file named HCV_rna_paired.txt exist? Is it in the directory from which you run this R script? $\endgroup$
    – terdon
    Feb 5 '21 at 17:23
  • $\begingroup$ Not a Windows user anymore for almost 15 years now but doesn't Win use backslashes to delimit paths and folders? $\endgroup$
    – ATpoint
    Feb 6 '21 at 15:07
  • $\begingroup$ Yes the file exists in the same directory in which I was running commands. As for the error message, would I receive the same message if it was a path error? I will try this next. $\endgroup$
    – hko
    Feb 6 '21 at 20:47
  • $\begingroup$ Definitely a file not found problem. Try: mydat<-scan("HCV_rna_paired.txt",what="",n=10) and see if it gives the same error $\endgroup$ Feb 8 '21 at 8:03

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