fastq files
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David ▴ 860
@david-3335
Last seen 6.7 years ago
Hi, I have the following fastq header: @ILLUMINA-E6F4B9_0000:5:1:1184:949#0/1 NGGGCTGGGTCGGTCGGGC +ILLUMINA-E6F4B9_0000:5:1:1184:949#0/1 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB Does any of the R packages (e.g: shortread) can convert this fastq to fasta file ? thanks, david
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@martin-morgan-1513
Last seen 5 months ago
United States
On 03/11/2011 05:42 AM, David martin wrote: > Hi, > I have the following fastq header: > > @ILLUMINA-E6F4B9_0000:5:1:1184:949#0/1 > NGGGCTGGGTCGGTCGGGC > +ILLUMINA-E6F4B9_0000:5:1:1184:949#0/1 > BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB > > Does any of the R packages (e.g: shortread) can convert this fastq to > fasta file ? Hi David -- In Biostrings write.XStringSet(read.XStringSet(fromFile, format="fastq"), toFile) in ShortRead writeFasta(readFastq(fromFile), toFile) both read the entire file into memory. Martin > > thanks, > david > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
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Hi David, Martin, Actually read.DNAStringSet() has the 'nrec' and 'skip' arguments to let you read a subset of the FASTQ records. Cheers, H. On 03/11/2011 05:48 AM, Martin Morgan wrote: > On 03/11/2011 05:42 AM, David martin wrote: >> Hi, >> I have the following fastq header: >> >> @ILLUMINA-E6F4B9_0000:5:1:1184:949#0/1 >> NGGGCTGGGTCGGTCGGGC >> +ILLUMINA-E6F4B9_0000:5:1:1184:949#0/1 >> BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB >> >> Does any of the R packages (e.g: shortread) can convert this fastq to >> fasta file ? > > Hi David -- > > In Biostrings > > write.XStringSet(read.XStringSet(fromFile, format="fastq"), toFile) > > in ShortRead > > writeFasta(readFastq(fromFile), toFile) > > both read the entire file into memory. > > Martin > >> >> thanks, >> david >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
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library(Biostrings) fromFile="myfile.fastq" toFile="output.fa" > write.XStringSet(read.XStringSet(fromFile, format="fastq"), toFile) Error in is(x, "XStringSet") : could not find function "read.XStringSet" ANy idea ? On 03/11/2011 02:48 PM, Martin Morgan wrote: > On 03/11/2011 05:42 AM, David martin wrote: >> Hi, >> I have the following fastq header: >> >> @ILLUMINA-E6F4B9_0000:5:1:1184:949#0/1 >> NGGGCTGGGTCGGTCGGGC >> +ILLUMINA-E6F4B9_0000:5:1:1184:949#0/1 >> BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB >> >> Does any of the R packages (e.g: shortread) can convert this fastq to >> fasta file ? > > Hi David -- > > In Biostrings > > write.XStringSet(read.XStringSet(fromFile, format="fastq"), toFile) > > in ShortRead > > writeFasta(readFastq(fromFile), toFile) > > both read the entire file into memory. > > Martin > >> >> thanks, >> david >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >
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On 03/11/2011 06:06 AM, David martin wrote: > library(Biostrings) > > fromFile="myfile.fastq" > toFile="output.fa" > >> write.XStringSet(read.XStringSet(fromFile, format="fastq"), toFile) > Error in is(x, "XStringSet") : could not find function "read.XStringSet" > > ANy idea ? Type read. and then tab key -- correct is read.DNAStringSet / write.XStringSet, sorry. Martin > > > > > > On 03/11/2011 02:48 PM, Martin Morgan wrote: >> On 03/11/2011 05:42 AM, David martin wrote: >>> Hi, >>> I have the following fastq header: >>> >>> @ILLUMINA-E6F4B9_0000:5:1:1184:949#0/1 >>> NGGGCTGGGTCGGTCGGGC >>> +ILLUMINA-E6F4B9_0000:5:1:1184:949#0/1 >>> BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB >>> >>> Does any of the R packages (e.g: shortread) can convert this fastq to >>> fasta file ? >> >> Hi David -- >> >> In Biostrings >> >> write.XStringSet(read.XStringSet(fromFile, format="fastq"), toFile) >> >> in ShortRead >> >> writeFasta(readFastq(fromFile), toFile) >> >> both read the entire file into memory. >> >> Martin >> >>> >>> thanks, >>> david >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
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Cool, thanks On 03/11/2011 03:10 PM, Martin Morgan wrote: > On 03/11/2011 06:06 AM, David martin wrote: >> library(Biostrings) >> >> fromFile="myfile.fastq" >> toFile="output.fa" >> >>> write.XStringSet(read.XStringSet(fromFile, format="fastq"), toFile) >> Error in is(x, "XStringSet") : could not find function "read.XStringSet" >> >> ANy idea ? > > Type read. and then tab key -- correct is read.DNAStringSet / > write.XStringSet, sorry. Martin > >> >> >> >> >> >> On 03/11/2011 02:48 PM, Martin Morgan wrote: >>> On 03/11/2011 05:42 AM, David martin wrote: >>>> Hi, >>>> I have the following fastq header: >>>> >>>> @ILLUMINA-E6F4B9_0000:5:1:1184:949#0/1 >>>> NGGGCTGGGTCGGTCGGGC >>>> +ILLUMINA-E6F4B9_0000:5:1:1184:949#0/1 >>>> BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB >>>> >>>> Does any of the R packages (e.g: shortread) can convert this fastq to >>>> fasta file ? >>> >>> Hi David -- >>> >>> In Biostrings >>> >>> write.XStringSet(read.XStringSet(fromFile, format="fastq"), toFile) >>> >>> in ShortRead >>> >>> writeFasta(readFastq(fromFile), toFile) >>> >>> both read the entire file into memory. >>> >>> Martin >>> >>>> >>>> thanks, >>>> david >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >
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