QuasR error usign preprocessReads
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Paul Ríos • 0
@paul-rios-9604
Last seen 5.8 years ago
Perú

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

quasr error • 949 views
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Entering edit mode
Mike Smith ★ 5.2k
@mike-smith
Last seen 3 hours ago
EMBL Heidelberg / de.NBI

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.

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Entering edit mode
Paul Ríos • 0
@paul-rios-9604
Last seen 5.8 years ago
Perú

Thank you for the clarification! That works.

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