[BioC] Transfer Fasta to Fastq

[Chris Fields]

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