Oops - I didn't do reply all. ---- Original message ---- >Date: Tue, 14 Sep 2010 22:10:55 -0700 >From: "Kunbin Qu" <[email protected]> >Subject: RE: [Bioc-sig-seq] qa error in ShortRead >To: <[email protected]> > >Thanks a lot, Dario. I was reading the pdf of ShortRead which has such >usage. I tried what you suggested, it worked beautifully! > > >-----Original Message----- >From: Dario Strbenac [mailto:[email protected]] >Sent: Tuesday, September 14, 2010 10:00 PM >To: Kunbin Qu >Subject: Re: [Bioc-sig-seq] qa error in ShortRead > >Hi, > >qa can't be used on an object that you've created in R. You have to do >quality assessment from disk. Also, you weren't telling the qa function >which type of data you were giving it. > >You need : qa("./", "tmp2", type = "fastq") > >-------------------------------------- >Dario Strbenac >Research Assistant >Cancer Epigenetics >Garvan Institute of Medical Research >Darlinghurst NSW 2010 >Australia > > >---- Original message ---- >>Date: Tue, 14 Sep 2010 21:27:10 -0700 >>From: [email protected] (on behalf of "Kunbin >Qu" <[email protected]>) >>Subject: [Bioc-sig-seq] qa error in ShortRead >>To: <[email protected]> >> >>Hi, >> >>I received the following error when I tried to read some fastq in and >>generate QA report. Could anybody help me? Thanks. >> >>-Kunbin >> >> >>[srp101]more tmp2 >>@SEQUENCER01_0007:1:1:1066:13331#0/1 >>CAGCTANCTGCGTTCTTCATCGACGCACGAGCCGAGTATTAATGTGAATTG >>+SEQUENCER01_0007:1:1:1066:13331#0/1 >>fdfffcBccccccccfffffffeffffffcfffffedcfcffffddedfdd >>@SEQUENCER01_0007:1:1:1066:8699#0/1 >>CTTACCNCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCAC >>+SEQUENCER01_0007:1:1:1066:8699#0/1 >>cc^ccaBV]]ba_^Zc^cbaa`c`cL^```cb\ccc^aaaaa^aabba`bb >>@SEQUENCER01_0007:1:1:1066:20185#0/1 >>GCCACANACACCTGATTATCAACAGCCCGGCTTCGCTGAAGTAACTCCCAA >>+SEQUENCER01_0007:1:1:1066:20185#0/1 >>fffffbBbbbcccccfffffefffffffffeffffffffefffffdefffd >>[srp101] >> >> >>> s6<-readFastq("./", "tmp2") >>> q6<-qa(s6) >>Error: UserArgumentMismatch >> 'lane' must be 'character(1)' >> >> >>> sessionInfo() >>R version 2.11.0 (2010-04-22) >>x86_64-unknown-linux-gnu >> >>locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >>[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >>attached base packages: >>[1] stats graphics grDevices utils datasets methods base >> >> >>other attached packages: >>[1] ShortRead_1.6.2 Rsamtools_1.0.1 lattice_0.18-8 >>[4] Biostrings_2.16.7 GenomicRanges_1.0.1 IRanges_1.6.8 >> >>loaded via a namespace (and not attached): >>[1] Biobase_2.8.0 grid_2.11.0 hwriter_1.2 >>> >> >>______________________________________________________________________ >>The contents of this electronic message, including any attachments, are >intended only for the use of the individual or entity to which they are >addressed and may contain confidential information. If you are not the >intended recipient, you are hereby notified that any use, dissemination, >distribution, or copying of this message or any attachment is strictly >prohibited. If you have received this transmission in error, please send >an e-mail to [email protected] and delete this message, along >with any attachments, from your computer. >> >>_______________________________________________ >>Bioc-sig-sequencing mailing list >>[email protected] >>https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > >______________________________________________________________________ >The contents of this electronic message, including any attachments, are >intended only for the use of the individual or entity to which they are >addressed and may contain confidential information. If you are not the >intended recipient, you are hereby notified that any use, dissemination, >distribution, or copying of this message or any attachment is strictly >prohibited. If you have received this transmission in error, please send an >e-mail to [email protected] and delete this message, along with any >attachments, from your computer.
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