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
and
cat chr*.fa > hg19.fa

then I have run qAlign again and still get same error. I have confused what is wrong.

Hi

You don't say how you have definded "genomeFile". Nevertheless, try this:

proj <- qAlign(sampleFile, genome="BSgenome.Hsapiens.UCSC.hg19", maxHits=1, splicedAlignment=FALSE, alignmentsDir=results, clObj=cl, cacheDir=results)

Hope this helps, Hans-Rudolf

PS: and for future references: please include the output of  sessionInfo()