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 stoed in sampleFile. Currently this file cannot be read into the function. Not sure why.
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_rns_paired.txt