User: wang peter

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wang peter2.0k
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Posts by wang peter

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Comment: C: a program to force fastq using pred+33 scoring system
... dear Martin: thank you for your help on the some codiing. but i have a question about the function as(quality(reads), "numeric") the function quality must automatically identify the score system, phred+33 and phred+64. that is good on some cases, but if i processed the data in chunk. maybe a chu ...
written 3.5 years ago by wang peter2.0k
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Comment: C: a program to force fastq using pred+33 scoring system
... i am sorry, i have another question about the coding phred64 = rawToChar(as.raw(64:104)) phred33 = rawToChar(as.raw(33:73)) qual = chartr(phred64, phred33, quality(quality(reads))) how did it deal with quality score from 59 to 63? On Mon, May 19, 2014 at 9:32 PM, Wang Peter wrote: > thank ...
written 3.5 years ago by wang peter2.0k
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Comment: C: a program to force fastq using pred+33 scoring system
... thank you very much you coding is so beautiful, mine is ugly On Mon, May 19, 2014 at 8:03 PM, Martin Morgan wrote: > On 05/14/2014 02:56 PM, Wang Peter wrote: > >> i worte a program to automatically dectect the scoring system in fastq >> file >> and if pred+64, it should ...
written 3.5 years ago by wang peter2.0k
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a program to force fastq using pred+33 scoring system
... i worte a program to automatically dectect the scoring system in fastq file and if pred+64, it should be changed into pred+33 please help me make sure it is right rm(list=ls()) fastqfile="1.fastq"; working_dir="d:/working_dir" setwd(working_dir) library(ShortRead); reads <- readFastq(fastqfile) ...
written 3.5 years ago by wang peter2.0k • updated 3.5 years ago by Martin Morgan ♦♦ 20k
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how to change pred+33 to pred+44 in shortread
... library(ShortRead); reads <- readFastq(fastqfile); seqs <- sread(reads); qual <- quality(quality(reads)); score_sys = data.class(quality(reads));# cat("the quality score system (SFastqQuality=Phred+64,FastqQuality=Phred+33) is",score_sys,"\n") it is a Phred+ ...
written 3.5 years ago by wang peter2.0k
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Comment: C: a possible bug in the shortread packge
... thank you very much i think this method is not reliable if the data is high quality, no nt is low , like 59. they will be thought as SFastqQuality. i would u like to see if some score is higher than 80, then choose SFastqQuality. On Thu, May 15, 2014 at 3:56 AM, Martin Morgan wrote: > On 05/ ...
written 3.5 years ago by wang peter2.0k
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a possible bug in the shortread packge
... the coding can works well on many data. but when it works on 12 lines, i met such a problem how can the function tell the score if 33 or 64 system? library(ShortRead); reads <- readFastq(fastqfile); seqs <- sread(reads); score_sys = data.class(quality(reads)); cat("the quality score system ( ...
written 3.5 years ago by wang peter2.0k • updated 3.5 years ago by Martin Morgan ♦♦ 20k
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Comment: C: failed to install biocondoctuor
... thank you very much On Wed, Dec 4, 2013 at 1:55 AM, Dan Tenenbaum wrote: > PS. An easy way to select mirrors is to use the functions > chooseCRANmirror() > and > chooseBioCmirror() > > Dan > > > ----- Original Message ----- > > From: "Dan Tenenbaum" > > ...
written 4.0 years ago by wang peter2.0k
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failed to install biocondoctuor
... i just reinstall the biocondoctuor in china. it is very slow, due to chinese restriction to foreign website and i meet such error, i never met before package ‘annotate’ successfully unpacked and MD5 sums checked Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : cannot ...
written 4.0 years ago by wang peter2.0k • updated 4.0 years ago by Dan Tenenbaum ♦♦ 8.2k
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Comment: C: the
... sorry, i tried many versions,i can only list one of them: > sessionInfo() R version 2.15.2 (2012-10-26) Platform: x86_64-redhat-linux-gnu (64-bit) 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=en_US.UTF-8 LC_MESSA ...
written 4.1 years ago by wang peter2.0k

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