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

This is a bit confusing: the link you give above points to the cutadapt paper in the reference list of a paper about "ve-SEQ". The "ve-SEQ" paper seems to cite our QuasR package (reference 20), but my guess is that this citation is incorrect. The relevant text says:

"De-multiplexed sequence read-pairs were trimmed of low-quality bases using QUASR v7.01 [20] and adapter sequences with CutAdapt version 1.7.1 [21] and subsequently discarded if either read had less than 50b remaining sequence or if both reads matched the human reference sequence using Bowtie version 2.2.4 [22]."

The reason why I think this is a mixup is that there is no version 7.01 of QuasR (the current, most recent release version is 1.30). Also, QuasR does not support Bowtie version 2.

Could it be that the correct reference was https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3678329/ , which describes the software http://sourceforge.net/projects/quasr (most recent version is 7.01 from June 2012)? Unfortunately the two have the same name...

In any case, the above error most likely indicates that the file "HCV_rna_paired.txt" does not exist in the current working directory of your R process (you can obtain that using getwd()).