I added a new line character at the end of the file echo >> reads.fq I got the same numbers when I repeated the analysis
________________________________ From: Martin Morgan <mtmor...@fhcrc.org> Cc: bioc-sig-sequencing@r-project.org Sent: Wed, March 23, 2011 7:44:40 PM Subject: Re: [Bioc-sig-seq] readFastq() error On 03/23/2011 05:49 PM, joseph wrote: > Hi Martin > here is what I got: > x = readLines('~/myDir/reads.fq') > rd = x[c(FALSE, TRUE, FALSE, FALSE)] > qual = x[c(FALSE, FALSE, FALSE, TRUE)] > > which(nchar(rd) != nchar(qual)) > [1] 16509910 > # that is all the reads in the file > # When I tried to count the reads with the same number of characters, I > also got all the reads > > length(which(nchar(rd) == nchar(qual))) > [1] 16509909 I suspect there is a missing end-of-line on the last line of the file. > > Joseph > > > > ------------------------------------------------------------------------ > *From:* Martin Morgan <mtmor...@fhcrc.org> > *Cc:* bioc-sig-sequencing@r-project.org > *Sent:* Wed, March 23, 2011 4:21:25 PM > *Subject:* Re: [Bioc-sig-seq] readFastq() error > > On 03/23/2011 04:07 PM, Martin Morgan wrote: > > On 03/23/2011 03:58 PM, joseph wrote: > >> Hello > >> How would you fix a FASTQ file that gives the following error when > >> read with > >> readFastq()? > >> Other lanes from the same flow cell are imported fine with readFastq(). > >> > >> rfq = readFastq("~/myDir", pattern="reads.fq") > >> Error: Input/Output > >> file(s): > >> ~/myDir/reads.fq > >> message: IncompatibleTypes > >> message: invalid class "ShortReadQ" object: some sread and quality > widths > >> differ > >> > > > > you could read the file in > > > > x = readLines('~/myDir/reads.fq') > > > > split it into reads and qualities > > > > rd = x[c(FALSE, TRUE, FALSE, FALSE)] > > qual = x[c(FALSE, FALSE, TRUE, FALSE)] > > oops, x[c(FALSE, FALSE, FALSE, TRUE)] > > > > > and ask which have different numbers of characters > > > > which(nchar(rd) != nchar(qual)) > > > > Martin > > > >> head reads.fq > >> @GAII_0001:6:1:0:101#0/1 > >> NCTCANCATTGTTTGGACGGAACAAAACCGGGGACAATCT > >> +GAII_0001:6:1:0:101#0/1 > >> BX[_\B_VXGQQU]]]YTPMGWTZZTVQ_X[TGYPZG[WZ > >> @GAII_0001:6:1:0:123#0/1 > >> NGTGANTCNGCTCATTGCGAGTTTTAACCTTTTCTCTATC > >> +GAII_0001:6:1:0:123#0/1 > >> BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB > >> @GAII_0001:6:1:0:168#0/1 > >> NCCAGNCCCAGCAGCCCTTCCTTTTCCCTGCTTACCCTCA > >> > >> > >> > >> [[alternative HTML version deleted]] > >> > >> _______________________________________________ > >> Bioc-sig-sequencing mailing list > >> Bioc-sig-sequencing@r-project.org > <mailto:Bioc-sig-sequencing@r-project.org> > >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > > > > > > -- > Computational Biology > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > Location: M1-B861 > Telephone: 206 667-2793 > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793 [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing