Hi Martin & Harris

It looks like the bioconductor packages that I am using are updated:

> sessionInfo()
R version 2.11.1 (2010-05-31)
i486-pc-linux-gnu

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] ShortRead_1.6.2     Rsamtools_1.0.7     lattice_0.18-8
[4] Biostrings_2.16.9   GenomicRanges_1.0.7 IRanges_1.6.6

loaded via a namespace (and not attached):
[1] Biobase_2.8.0 grid_2.11.1   hwriter_1.2


Also, this is error  I get while exporting to fasta file:
>  fa <-sread(trimmed)
Error in slot(object, "sread") :
  no slot of name "sread" for this object of class "DNAStringSet"


And while exporting using writeFastq:

>  writeFastq(trimmed,"trimmedseqs")
Error in function (classes, fdef, mtable)  :
  unable to find an inherited method for function "writeFastq", for
signature "DNAStringSet"

It would be great if you could suggest some other method to export the
trimmed object.
Thanks!

On Tue, Aug 17, 2010 at 11:52 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> "Harris A. Jaffee" <hj@jhu.edu> writes:
>
> > Hi.  For the record, trimLRPatterns is in Biostrings with an assist
> > from IRanges, not ShortRead.  You can view it as a complicated call
> > to substr(), having nothing to do with file input or output.
> >
> > Perhaps nothing was displayed by ?writeFastq because you didn't have
> > ShortRead loaded.
> >
> > In any case, the quality scores of your reads cannot apply to your
> > trimmed reads without, at least, trimming them in the same fashion.
>
> Hi Harris -- Probably confusing to Jess, but... ShortRead defines a
> method on trimLRPatterns that uses the ranges=TRUE argument, and then
> narrows (any) ShortRead object so that, in fact, the quality scores do
> reflect the trimming that occurs. See
>
>  library(ShortRead)
>  showMethods(trimLRPatterns, class="ShortRead", includeDef=TRUE)
>
> Martin
>
> > But note that trimLRPatterns ignores quality scores, and there is
> > no wrapper or alternative (that I know of) that incorporates them.
> >
> > On Aug 17, 2010, at 10:46 AM, JASREET HUNDAL wrote:
> >
> >> I am new to R and don't quiet understand this correctly. When I tried
> >> ?writeFastq , nothing is displayed.
> >> Is there is any other way to export the trimmed reads? I am using this
> >> workflow:
> >> http://www.bioconductor.org/help/workflows/high-throughput-sequencing/
> >>
> >> Thanks!
> >>
> >>
> >> On Mon, Aug 16, 2010 at 5:50 PM, Marcus Davy <mdavy86@gmail.com>
> >> wrote:
> >>
> >>> One option is to try writeFastq to fastq format, I believe it was
> >>> working
> >>> on recently and is fast.
> >>>
> >>> exptPath   <- system.file("extdata", package = "ShortRead")
> >>> sp         <- SolexaPath(exptPath)
> >>> fqpattern  <- "s_1_sequence.txt"
> >>> fl         <- file.path(analysisPath(sp), fqpattern)
> >>> fq         <- readFastq(sp, fqpattern)
> >>>
> >>> tf         <- tempfile(tmpdir="/tmp")
> >>>
> >>> writeFastq(fq, tf)
> >>>
> >>>
> >>> Marcus
> >>>
> >>>
> >>> On Tue, Aug 17, 2010 at 10:42 AM, JASREET HUNDAL
> >>> <jasreeth@gmail.com>wrote:
> >>>
> >>>> Has anyone worked with trimLRPatterns function in the ShortRead
> >>>> library
> >>>> for
> >>>> adaptor trimming?
> >>>> What is the best way to export the trimmed reads in a fasta/fastq/
> >>>> text
> >>>> file?
> >>>> I have a large 5,000,000 line fastq file with 50bp reads as input.
> >>>> I have tried write.table as well as writeFASTA but nothing seems
> >>>> to be
> >>>> working.
> >>>> Hence, I would appreciate if somebody could help me out as I am
> >>>> novice in
> >>>> the world of R/Bioconductor.
> >>>>
> >>>> Thanks
> >>>> -Jess
> >>>>
> >>>>        [[alternative HTML version deleted]]
> >>>>
> >>>> _______________________________________________
> >>>> Bioc-sig-sequencing mailing list
> >>>> Bioc-sig-sequencing@r-project.org
> >>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
> >>>>
> >>>
> >>>
> >>
> >>      [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
> >> Bioc-sig-sequencing mailing list
> >> Bioc-sig-sequencing@r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
> >
> > _______________________________________________
> > Bioc-sig-sequencing mailing list
> > Bioc-sig-sequencing@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>
> --
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
>

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