[Bioc-sig-seq] readFastq() error

[Martin Morgan]

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)]

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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