I am very new in rna-seq analysis in R so I am sorry that I have confused somethings in the analysis.
I am using quasr package for hg19 genome. I have generated sample file and download BSgenome.Hsapiens.UCSC.hg19 for genome file. When I run
>proj <- qAlign(sampleFile, genome=genomeFile, maxHits=1, splicedAlignment=FALSE, alignmentsDir=results, clObj=cl, cacheDir=results)
command, I get an exactly error like this:
Error: The specified genome ./data/BSgenome.Hsapiens.UCSC.hg19 does not have the extension of a fasta file (fa,fasta,fna)
and then I have download chrom.Fa file and used this commands,
tar -zxvf chromFa.tar.gz
cat chr*.fa > hg19.fa
then I have run qAlign again and still get same error. I have confused what is wrong.