Steve , Thanks for such an elaborate explanation.. It sure cleared a lot of our concerns!
Martin, Thanks for resolving the issue with "trimmed" object...using subject=seq instead of subject=sread(seq)... I finally have a fastq file with my trimmed reads! :) Thanks to this thread my first experience with R & bioconductor, wasnt so bad ! :) -Jess On Tue, Aug 17, 2010 at 5:25 PM, Martin Morgan <[email protected]> wrote: > On 08/17/2010 02:55 PM, Steve Lianoglou wrote: > > Hi Jess, > > > > On Tue, Aug 17, 2010 at 5:15 PM, JASREET HUNDAL <[email protected]> > wrote: > >> Hi Martin & Harris > >> > >> It looks like the bioconductor packages that I am using are updated: > > ... > >> 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" > > My bad. The script Jess mention says > > trimmed <- trimLRPatterns(pcrPrimer, subject=sread(seq)) > > and then trimmed is a DNAStringSet (try class(trimmed)), and writeFastq > doesn't make sense. With > > trimmed <- trimLRPatterns(pcrPrimer, subject=seq) > > it's a ShortReadQ (i.e., including quality) and writeFastq(trimmed, > "/path/to/file") should work. Explanations Steve offers below still > apply to th DNAStringSet. > > Martin > > > > > The "sread" method is used to get the *reads* (which would be a > > DNAStringSet object ) out of a ShortRead* object. The ShortRead* class > > stores the reads, as well as other information about the reads (phred > > scores, etc.) > > > > It looks like your "trimmed" object is already a DNAStringSet -- so > > calling sread() on a DNAStringSet isn't really meaningful ... you > > would just get itself. > > > > In short, the "trimmed" object you have appears to the the > > DNAStringSet you are looking to get by using the "sread" function. > > > >> 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. > > > > Here you have the opposite problem. > > > > You "just" have a DNAStringSet -- no other metadata about your reads > > that a ShortRead* class holds, like phred scores, etc. > > > > The writeFastq file expects to write your object as a FASTQ file. > > > > If you have a DNAStringSet (which is what your "trimmed" object is), > > you can only really hope to write a FASTA file, in which case you can > > use the "writeFASTA" function (or the write.XStringSet function that > > Martin suggested) from the Biostrings package (which is already > > loaded). > > > > Does that make sense? > > > > So again (in summary (?)): > > the problem you are having is that you think that your "trimmed" > > object is something it's not. > > > > I'm not sure how you got it, or where it came from, but it is "just" a > > DNAStringSEt -- which is simply a number of sequences (reads). > > > > You can't write it as a fastq file (with writeFastq), and there's no > > need to get the "reads" out of it (with the sread function) because > > that's what they already are. > > > > Hope that helps, > > > > > -- > 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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
