# Trouble aligning next generation sequencing data to reference genomes using QuasR package in Bioconductor. Cannot import .txt

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

• Does the file named HCV_rna_paired.txt exist? Is it in the directory from which you run this R script? – terdon Feb 5 at 17:23
• Not a Windows user anymore for almost 15 years now but doesn't Win use backslashes to delimit paths and folders? – ATpoint Feb 6 at 15:07
• 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. – hko Feb 6 at 20:47
• Definitely a file not found problem. Try: mydat<-scan("HCV_rna_paired.txt",what="",n=10) and see if it gives the same error – Fabio Marroni Feb 8 at 8:03