[BioC] Transfer Fasta to Fastq

[Martin Morgan]

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]]
>>>>
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