Hi Peter,

Peter Cock wrote, On 03/29/2011 05:39 AM:
>> 2. the tools accepts FASTA, FASTQ in both Sanger and Illumina
>> format (no more need for grooming). Illumina is the default for
>> newly uploaded FASTQ files.
> I think that's a bad idea - use Sanger FASTQ as the default to be
> consistent with the rest of Galaxy, and also with CASAVA 1.8
> Illumina machines will produce that too, see:
> http://seqanswers.com/forums/showthread.php?t=8895

Thanks for the link - very interesting read, I wasn't aware of it.

However, for our local Galaxy server - I'm sticking with Illumina scale until I 
see real samples with phred-33 in the wild.

The defaults can be easily changed (in the XML file, simply assume a different 
scale when the extension is "fastq"),
or don't accept "fastq" at all and force the user to change the format to 
either "fastqillumina" or "fastqsanger".

I'll explain my reasoning:
We (at our lab) deal mostly with Illumina FASTQ files, with the Illumina scale.
I'm trying to make life as easy as possible for our users.
When they upload a FASTQ file, it is by default an Illumina FASTQ file, I want 
them to be able to use a workflow on it immediately.
All of our internal tools assume Illumina scale.

The one time I've tried to make the built-in Bowtie tool available, I got 
complaints about "why isn't my FASTQ file appear in the input list" - 
because it was "fastq" and not "fastqsanger" after grooming - this is a silly 
technical step that should not be a concern to users - so I'm taking it out of 
the equation here (not to mention that grooming two 14GB FASTQ files for every 
lane is a huge waste of space and time).

When CASAVA 1.8 is ready (that is - when it is actually running in our 
sequencing center), then we'll have to deal with it.
Ideally - galaxy will have some metadata code that will scan the first 
1,000,000 lines and heuristically detect which scale it is.
I'm not leaving this choice for the users, because they will make the wrong 
choice and then come crying back.

Just my two cents,
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