[Bioc-sig-seq] trimLRPatterns - adaptor trimming
mtmorgan at fhcrc.org
Tue Aug 17 18:52:51 CEST 2010
"Harris A. Jaffee" <hj at 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
showMethods(trimLRPatterns, class="ShortRead", includeDef=TRUE)
> 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
>> On Mon, Aug 16, 2010 at 5:50 PM, Marcus Davy <mdavy86 at gmail.com>
>>> One option is to try writeFastq to fastq format, I believe it was
>>> 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)
>>> On Tue, Aug 17, 2010 at 10:42 AM, JASREET HUNDAL
>>> <jasreeth at gmail.com>wrote:
>>>> Has anyone worked with trimLRPatterns function in the ShortRead
>>>> adaptor trimming?
>>>> What is the best way to export the trimmed reads in a fasta/fastq/
>>>> 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
>>>> Hence, I would appreciate if somebody could help me out as I am
>>>> novice in
>>>> the world of R/Bioconductor.
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