Hi,

On Wed, Apr 10, 2013 at 1:51 AM, carol white <wht_crl@yahoo.com> wrote:

> Hi,
> Is it normal not to have the same number of sequences in the fastq file
> and the object generated from readfastq?
>
> grep @ SRR062641.filt.fastq | wc -l
> 187786
>
>   data <- readFastq("SRR062641.filt.fastq")
>
> summary(data)
>     Length      Class       Mode
>     109811 ShortReadQ         S4
>

Isn't "@" a valid ASCII encoding for a phred score?

http://en.wikipedia.org/wiki/FASTQ_format#Encoding

What do you get when you divide `wc -l SRR062641.filt.fastq` by 4?

-steve

-- 
Steve Lianoglou
Defender of The Thesis
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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