qCount in QuasR for RNAseq quantification

Question

[tarek.mohamed]

Hi All,

I am using QuasR to analyze mt paired end RNAseq data, now I have bam files for my 12 samples and the next step is to generate a count table for Differential gene expression analysis. I followed the QuasR vignette and I used qCount() but I had a problem (R could not find my genome file)

sampleFile <- "DOX_RNAseq.txt"
genomeFile<-"BSgenome.Hsapiens.NCBI.GRCh38"
proj_RNASeq<- qAlign(sampleFile, genomeFile,cacheDir = "E:/Doxorubicin Project RNA-seq Data")

library(GenomicFeatures)
annotationFile <- "BSgenome.Hsapiens.NCBI.GRCh38_annotation.gtf"
chrLen <- scanFaIndex(genomeFile)

Error in scanFaIndex(open(FaFile(file))) :
  error in evaluating the argument 'file' in selecting a method for function 'scanFaIndex': Error in .io_check_exists(path(con)) : file(s) do not exist:
  'BSgenome.Hsapiens.NCBI.GRCh38'