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