"Harris A. Jaffee" <[email protected]> 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 <[email protected]> >> 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 >>> <[email protected]>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 >>>> [email protected] >>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >>>> >>> >>> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-sig-sequencing mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > 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 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
