0
$\begingroup$

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

Improve this question
$\endgroup$
4
  • 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 ♦
    Commented Feb 5, 2021 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? $\endgroup$
    – user3051
    Commented Feb 6, 2021 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
    Commented Feb 6, 2021 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 $\endgroup$
    – Fabio Marroni
    Commented Feb 8, 2021 at 8:03

0

Reset to default

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Browse other questions tagged or ask your own question.