I got an error: > names(sr) <- id(fq) Error in `names<-`(`*tmp*`, value = <S4 object of class "BStringSet">) : 'value' must be NULL or a character vector
________________________________ From: Martin Morgan <[email protected]> Cc: [email protected] Sent: Monday, August 3, 2009 7:06:56 PM Subject: Re: [Bioc-sig-seq] fastq2fasta Hi Joseph -- One way, for some file 'fin' to file 'fout' fq <- readFastq(fin) sr <- sread(fq) names(sr) <- id(fq) write.XStringSet(sr, fout, format="fasta") Martin joseph wrote: > Hello > Can you show me how to use ShortRead to convert a fastq file like this one > @7:1:1 > NNNNNNN > + > %%%%%% > @7:1:2 > NNNNNNN > + > %%%%%% > > to a fasta file keeping only the id and the read: > >> @7:1:1 > NNNNNNNN >> @7:1:2 > NNNNNNNN > > Thanks in advance > Joseph > > > > [[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
