[BioC] Transfer Fasta to Fastq

[Michael Dondrup]

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]]
>> 
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