[BioC] Transfer Fasta to Fastq

[Michael Dondrup]

Yes there is one,

just figured out the writeFastQ method for ShortRead. So here is a code example, because it wasn't quite clear for me how to
feed the the read454 function with data in the correct way, maybe there should be a better example in the documentation (eg. this ):

> rpath = RochePath(experimentPath="/directory/with/fna+qual/")
> reads = read454(rpath)
Read 460210 items
> writeFastq(reads, file="~/out.fastq")

It wa not quite clear to me from the docu what happens if there are multiple files in that directory, I guess just one is taken?

Best
Michael

On Nov 24, 2010, at 3:42 PM, Michael Lawrence wrote:

> The read454 function in ShortRead will parse fasta and qual files into a ShortReadQ. No trivial way to write that out as a fastq, but it could be done.
> 
> On Wed, Nov 24, 2010 at 5:50 AM, Michael Dondrup <Michael.Dondrup at uni.no> wrote:
> Hi,
> if you got fasta + qual files, there is an example perl script here:
> http://biostar.stackexchange.com/questions/2774/how-to-convert-454-data-to-sam-format/2778#2778
> have nothing in R yet, but that shows the principle and could be easily done in R. If you don't have a qual file,
> you will have to make the values up using eg. some constant values.
> 
> Using an offset of 33 gives you Sanger style quality code, while -i think- using offset 64 should yield Illumina
> score codes.
> 
> Best
> Michael
> 
> On Nov 24, 2010, at 2:36 PM, Chris Fields wrote:
> 
> > Just curious, but where would the quality score information come from?  Or do you have them in a separate .qual file?
> >
> > chris
> >
> > On Nov 24, 2010, at 5:56 AM, Bin Ma wrote:
> >
> >> Dear all,
> >>
> >> Is there any function can transfer Fasta to Fastq file.
> >>
> >>
> >> With Best Regards
> >>
> >> Bin Ma
> >> --------------------------------------------------
> >> http://lvandma.wordpress.com
> >> Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition,
> >> College of Environmental and Natural Resource Sciences,
> >> Zhejiang University, Hangzhou 310029, China
> >>
> >>      [[alternative HTML version deleted]]
> >>
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