I have fastq files from a paired end sequencing, so I would like to prepare the input sequence(remove adapters and N bases) before to do the alignment. So I ran the next commands but it shows a error:

infiles <- system.file(package="QuasR", "extdata",
                       c("nsc0001_S1_L001_R1_001.fastq.gz", "nsc0001_S1_L001_R2_001.fastq.gz"))

outfiles <- paste(tempfile(pattern=c("output_1.fastq","output_2.fastq")),sep="")

preprocessReads(filename=infiles[1],
                outputFilename="output_1.fastq",
                filenameMate=infiles[2],
                outputFilenameMate=outfiles[2],
                nBases=0, complexity=0.6)

Error in preprocessReads(filename = infiles[1], outputFilename = "output_1.fastq",  : 
  unsupported file format (must be one of 'fasta' or 'fastq')

Could someone help me with this?

Thank you

Admittedly the error message is misleading, but the files you're trying to read don't exist.

> library(QuasR)
> infiles <- system.file(package="QuasR", "extdata", c("nsc0001_S1_L001_R1_001.fastq.gz", "nsc0001_S1_L001_R2_001.fastq.gz"))
> infiles
[1] ""

You more likely want something like:

infiles <- file.path("/here/is/my/data", c("nsc0001_S1_L001_R1_001.fastq.gz", "nsc0001_S1_L001_R2_001.fastq.gz"))

where "/here/is/my/data" is the path to the folder containing the fastq files you're trying to analyse.

Thank you for the clarification! That works.