Transfer Fasta to Fastq
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Bin Ma ▴ 20
@bin-ma-4363
Last seen 9.9 years ago
Dear all, Is there any function can transfer Fasta to Fastq file. With Best Regards Bin Ma -------------------------------------------------- http://lvandma.wordpress.com Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, College of Environmental and Natural Resource Sciences, Zhejiang University, Hangzhou 310029, China [[alternative HTML version deleted]]
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Bin Ma ▴ 20
@bin-ma-4363
Last seen 9.9 years ago
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Just curious, but where would the quality score information come from? Or do you have them in a separate .qual file? chris On Nov 24, 2010, at 5:56 AM, Bin Ma wrote: > Dear all, > > Is there any function can transfer Fasta to Fastq file. > > > With Best Regards > > Bin Ma > -------------------------------------------------- > http://lvandma.wordpress.com > Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, > College of Environmental and Natural Resource Sciences, > Zhejiang University, Hangzhou 310029, China > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Hi, if you got fasta + qual files, there is an example perl script here: http://biostar.stackexchange.com/questions/2774/how-to-convert-454 -data-to-sam-format/2778#2778 have nothing in R yet, but that shows the principle and could be easily done in R. If you don't have a qual file, you will have to make the values up using eg. some constant values. Using an offset of 33 gives you Sanger style quality code, while -i think- using offset 64 should yield Illumina score codes. Best Michael On Nov 24, 2010, at 2:36 PM, Chris Fields wrote: > Just curious, but where would the quality score information come from? Or do you have them in a separate .qual file? > > chris > > On Nov 24, 2010, at 5:56 AM, Bin Ma wrote: > >> Dear all, >> >> Is there any function can transfer Fasta to Fastq file. >> >> >> With Best Regards >> >> Bin Ma >> -------------------------------------------------- >> http://lvandma.wordpress.com >> Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, >> College of Environmental and Natural Resource Sciences, >> Zhejiang University, Hangzhou 310029, China >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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The read454 function in ShortRead will parse fasta and qual files into a ShortReadQ. No trivial way to write that out as a fastq, but it could be done. On Wed, Nov 24, 2010 at 5:50 AM, Michael Dondrup <michael.dondrup@uni.no>wrote: > Hi, > if you got fasta + qual files, there is an example perl script here: > > http://biostar.stackexchange.com/questions/2774/how-to-convert-454 -data-to-sam-format/2778#2778 > have nothing in R yet, but that shows the principle and could be easily > done in R. If you don't have a qual file, > you will have to make the values up using eg. some constant values. > > Using an offset of 33 gives you Sanger style quality code, while -i think- > using offset 64 should yield Illumina > score codes. > > Best > Michael > > On Nov 24, 2010, at 2:36 PM, Chris Fields wrote: > > > Just curious, but where would the quality score information come from? > Or do you have them in a separate .qual file? > > > > chris > > > > On Nov 24, 2010, at 5:56 AM, Bin Ma wrote: > > > >> Dear all, > >> > >> Is there any function can transfer Fasta to Fastq file. > >> > >> > >> With Best Regards > >> > >> Bin Ma > >> -------------------------------------------------- > >> http://lvandma.wordpress.com > >> Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant > Nutrition, > >> College of Environmental and Natural Resource Sciences, > >> Zhejiang University, Hangzhou 310029, China > >> > >> [[alternative HTML version deleted]] > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor@stat.math.ethz.ch > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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On 11/24/2010 06:42 AM, Michael Lawrence wrote: > The read454 function in ShortRead will parse fasta and qual files into a > ShortReadQ. No trivial way to write that out as a fastq, but it could be > done. ShortRead::writeFastq Also ?ShortReadQ to construct piece together the fasta / fastq components if they're from separate fasta-style files Martin > > On Wed, Nov 24, 2010 at 5:50 AM, Michael Dondrup <michael.dondrup at="" uni.no="">wrote: > >> Hi, >> if you got fasta + qual files, there is an example perl script here: >> >> http://biostar.stackexchange.com/questions/2774/how-to-convert-454 -data-to-sam-format/2778#2778 >> have nothing in R yet, but that shows the principle and could be easily >> done in R. If you don't have a qual file, >> you will have to make the values up using eg. some constant values. >> >> Using an offset of 33 gives you Sanger style quality code, while -i think- >> using offset 64 should yield Illumina >> score codes. >> >> Best >> Michael >> >> On Nov 24, 2010, at 2:36 PM, Chris Fields wrote: >> >>> Just curious, but where would the quality score information come from? >> Or do you have them in a separate .qual file? >>> >>> chris >>> >>> On Nov 24, 2010, at 5:56 AM, Bin Ma wrote: >>> >>>> Dear all, >>>> >>>> Is there any function can transfer Fasta to Fastq file. >>>> >>>> >>>> With Best Regards >>>> >>>> Bin Ma >>>> -------------------------------------------------- >>>> http://lvandma.wordpress.com >>>> Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant >> Nutrition, >>>> College of Environmental and Natural Resource Sciences, >>>> Zhejiang University, Hangzhou 310029, China >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > 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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Yes there is one, just figured out the writeFastQ method for ShortRead. So here is a code example, because it wasn't quite clear for me how to feed the the read454 function with data in the correct way, maybe there should be a better example in the documentation (eg. this ): > rpath = RochePath(experimentPath="/directory/with/fna+qual/") > reads = read454(rpath) Read 460210 items > writeFastq(reads, file="~/out.fastq") It wa not quite clear to me from the docu what happens if there are multiple files in that directory, I guess just one is taken? Best Michael On Nov 24, 2010, at 3:42 PM, Michael Lawrence wrote: > The read454 function in ShortRead will parse fasta and qual files into a ShortReadQ. No trivial way to write that out as a fastq, but it could be done. > > On Wed, Nov 24, 2010 at 5:50 AM, Michael Dondrup <michael.dondrup at="" uni.no=""> wrote: > Hi, > if you got fasta + qual files, there is an example perl script here: > http://biostar.stackexchange.com/questions/2774/how-to-convert-454 -data-to-sam-format/2778#2778 > have nothing in R yet, but that shows the principle and could be easily done in R. If you don't have a qual file, > you will have to make the values up using eg. some constant values. > > Using an offset of 33 gives you Sanger style quality code, while -i think- using offset 64 should yield Illumina > score codes. > > Best > Michael > > On Nov 24, 2010, at 2:36 PM, Chris Fields wrote: > > > Just curious, but where would the quality score information come from? Or do you have them in a separate .qual file? > > > > chris > > > > On Nov 24, 2010, at 5:56 AM, Bin Ma wrote: > > > >> Dear all, > >> > >> Is there any function can transfer Fasta to Fastq file. > >> > >> > >> With Best Regards > >> > >> Bin Ma > >> -------------------------------------------------- > >> http://lvandma.wordpress.com > >> Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, > >> College of Environmental and Natural Resource Sciences, > >> Zhejiang University, Hangzhou 310029, China > >> > >> [[alternative HTML version deleted]] > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor at stat.math.ethz.ch > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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On Wed, Nov 24, 2010 at 7:43 AM, Michael Dondrup <michael.dondrup@uni.no>wrote: > Yes there is one, > > just figured out the writeFastQ method for ShortRead. So here is a code > example, because it wasn't quite clear for me how to > feed the the read454 function with data in the correct way, maybe there > should be a better example in the documentation (eg. this ): > > > rpath = RochePath(experimentPath="/directory/with/fna+qual/") > > reads = read454(rpath) > Read 460210 items > > writeFastq(reads, file="~/out.fastq") > > It wa not quite clear to me from the docu what happens if there are > multiple files in that directory, I guess just one is taken? > > As is the convention with ShortRead, all files matching the pattern are concatenated into the resulting ShortReadQ object. If you want to read a single file, use the complete path to the file. Also, the readFastaQual alias for that function might be conceptually more appropriate if you're not dealing with 454 data. > Best > Michael > > On Nov 24, 2010, at 3:42 PM, Michael Lawrence wrote: > > > The read454 function in ShortRead will parse fasta and qual files into a > ShortReadQ. No trivial way to write that out as a fastq, but it could be > done. > > > > On Wed, Nov 24, 2010 at 5:50 AM, Michael Dondrup <michael.dondrup@uni.no> > wrote: > > Hi, > > if you got fasta + qual files, there is an example perl script here: > > > http://biostar.stackexchange.com/questions/2774/how-to-convert-454 -data-to-sam-format/2778#2778 > > have nothing in R yet, but that shows the principle and could be easily > done in R. If you don't have a qual file, > > you will have to make the values up using eg. some constant values. > > > > Using an offset of 33 gives you Sanger style quality code, while -i > think- using offset 64 should yield Illumina > > score codes. > > > > Best > > Michael > > > > On Nov 24, 2010, at 2:36 PM, Chris Fields wrote: > > > > > Just curious, but where would the quality score information come from? > Or do you have them in a separate .qual file? > > > > > > chris > > > > > > On Nov 24, 2010, at 5:56 AM, Bin Ma wrote: > > > > > >> Dear all, > > >> > > >> Is there any function can transfer Fasta to Fastq file. > > >> > > >> > > >> With Best Regards > > >> > > >> Bin Ma > > >> -------------------------------------------------- > > >> http://lvandma.wordpress.com > > >> Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant > Nutrition, > > >> College of Environmental and Natural Resource Sciences, > > >> Zhejiang University, Hangzhou 310029, China > > >> > > >> [[alternative HTML version deleted]] > > >> > > >> _______________________________________________ > > >> Bioconductor mailing list > > >> Bioconductor@stat.math.ethz.ch > > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > > >> Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@stat.math.ethz.ch > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > [[alternative HTML version deleted]]
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In my opinion, it's always best to convert to Sanger-based FASTQ if possible. IIRC that is what most archive resources (SRA, etc) currently support, it's now spec'ed in a publication (so you can at least point to that and blame the authors if something isn't correct :) Not to mention it's fairly difficult to discern between the variant FASTQ forms based on the quality string alone. http://www.ncbi.nlm.nih.gov/pubmed/20015970?dopt=Abstract chris (full disclosure, one of the co-authors on that paper) On Nov 24, 2010, at 7:50 AM, Michael Dondrup wrote: > Hi, > if you got fasta + qual files, there is an example perl script here: > http://biostar.stackexchange.com/questions/2774/how-to-convert-454 -data-to-sam-format/2778#2778 > have nothing in R yet, but that shows the principle and could be easily done in R. If you don't have a qual file, > you will have to make the values up using eg. some constant values. > > Using an offset of 33 gives you Sanger style quality code, while -i think- using offset 64 should yield Illumina > score codes. > > Best > Michael > > On Nov 24, 2010, at 2:36 PM, Chris Fields wrote: > >> Just curious, but where would the quality score information come from? Or do you have them in a separate .qual file? >> >> chris >> >> On Nov 24, 2010, at 5:56 AM, Bin Ma wrote: >> >>> Dear all, >>> >>> Is there any function can transfer Fasta to Fastq file. >>> >>> >>> With Best Regards >>> >>> Bin Ma >>> -------------------------------------------------- >>> http://lvandma.wordpress.com >>> Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, >>> College of Environmental and Natural Resource Sciences, >>> Zhejiang University, Hangzhou 310029, China >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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