[Bioc-sig-seq] trimLRPatterns - adaptor trimming

[Harris A. Jaffee]

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.

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 at 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 at 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
>>>
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>>>
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>>
>>
>
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