[Bioperl-l] Next-gen modules

[Chris Fields]

On Jun 24, 2009, at 11:27 AM, Peter wrote:

> On Wed, Jun 24, 2009 at 5:22 PM, Chris Fields<cjfields at illinois.edu>  
> wrote:
>>> So when you say "fastqint" are you talking about something else?
>>> Could you show us an example record in this format?
>>>
>>> Peter
>>
>> The same as fastq, except the ASCII quality is converted to actual  
>> score:
>>
>> @4_1_912_360
>> AAGGGGCTAGAGAAACACGTAATGAAGGGAGGACTC
>> +4_1_912_360
>> 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 21 40 40  
>> 40 40 40
>> 40 40 40 40 26 40 40 14 39 40 40
>> @4_1_54_483
>> TAATAAATGTGCTTCCTTGATGCATGTGCTATGATT
>> +4_1_54_483
>> 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 16 40 40  
>> 40 28 40
>> 40 40 40 40 40 16 40 40 5 40 40
>
> OK - and who uses this "Integer FASTQ" files?
>
> Peter

Not sure, but it is covered by MAQ via the conversion script (as FASTQ- 
int):

http://maq.sourceforge.net/fq_all2std.pl

chris