ShortRead ,WriteFastq File?

[bio_jit]

oparetingSystem windows7, 64bit, sp1
R.Version = 3.0.2
biocVersion = 1.12.0

I made random sample by using ShortRead, FastqSampler

>sampler<- FastqSampler("./Sequencing/ERR127306_1.fastq.gz")
Fq<-yield(sampler)

now I want to write this in a fatsq file and save how to do?
i did
writeFastq(object="Fq", file="./Sequencing/sample.fastq", mode="w")
and get error

Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘writeFastq’ for signature ‘"character", "character"’

any body plz. help I need it badly; please mind that I am a new comer in this area so kindly explain what you are doing.

[dpryan]

Try:

writeFastq(object=Fq, file="./Sequencing/sample.fastq", mode="w")

The quotes around "Fq" make it a character vector rather than an object.

[bio_jit]

Thanks ! thank you a lot ! u saved me!

[dpryan]

No worries, glad you got things working!

[bio_jit]

Help Plz!

Hi Ryan ,

sorry to disturb you once again but I just stuck. Plz. help me

I got a small program to spit a big fatsq files in 100000 reads/file and put them new names automatically. The program is working nice but I want to save the files in other folder , say ./Sequencing/output. tried several ways but not working. plz. help

my program


# set the file
FastqFile <- "./Sequencing/ERR127306_1.fastq.gz"
fileBaseName <- sub(".fastq$","", FastqFile)
# iterate over fastq file
f <- FastqStreamer(FastqFile, 1000000)
file_index <- 0
while (length(fq <- yield(f))) {
newName <- paste( fileBaseName, "_", file_index,".fastq", sep="")
writeFastq(fq, file=newName)
file_index <- file_index + 1
}
close(f)

[dpryan]

Just put the directory in the "newName" string. So:

 newName <- paste(newDirectory, "/", fileBaseName, "_", file_index,".fastq", sep="")