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>
*To:* joseph <jdsan...@yahoo.com>
*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]]
>>
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>
>
--
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
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