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
Joseph
________________________________
From: Martin Morgan <[email protected]>
Cc: [email protected]
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]]
>>
>> _______________________________________________
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>> [email protected]
>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>
>
--
Computational Biology
Fred Hutchinson Cancer Research Center
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Telephone: 206 667-2793
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