Question

number of sequence from readfastq

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carol white ▴ 680

@carol-white-2174

Last seen 9.6 years ago

European Union

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 Thanks, Carol [[alternative HTML version deleted]]

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ADD COMMENT • link updated 11.7 years ago by Steve Lianoglou ★ 13k • written 11.7 years ago by carol white ▴ 680

score 0 · Answer 1 · 2013-04-09

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Steve Lianoglou ★ 13k

@steve-lianoglou-2771

Last seen 22 months ago

United States

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 [[alternative HTML version deleted]]

ADD COMMENT • link 11.7 years ago Steve Lianoglou ★ 13k

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I get 109811 Thank you very much for all replies, ________________________________ From: Steve Lianoglou <mailinglist.honeypot@gmail.com> Cc: "bioconductor@stat.math.ethz.ch" <bioconductor@stat.math.ethz.ch> Sent: Wednesday, April 10, 2013 11:08 AM Subject: Re: [BioC] number of sequence from readfastq Hi, 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 [[alternative HTML version deleted]]

ADD REPLY • link 11.7 years ago carol white ▴ 680