Thanks Ross, I don't see it under my local install - are there any pre-written 
scripts to integrate it with a local galaxy instance?

I assume you are talking about this tool here:
http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/

 -John

________________________________________
From: Ross [ross.laza...@gmail.com]
Sent: Wednesday, June 01, 2011 11:41 AM
To: John David Osborne
Cc: galaxy-u...@bx.psu.edu
Subject: Re: [galaxy-user] FastQ Groomer and Compute Quality Statistics

You can avoid the space/time overhead of grooming and get
comprehensive QC reports using the new wrapper for FastQC (under NGS:
QC) - it takes fastq of any flavour (and bam) groomed or not,
producing a superset of the compute quality stats output without the
need for an intermediate step. Highly recommended.

On Wed, Jun 1, 2011 at 12:02 PM, John David Osborne <ozb...@uab.edu> wrote:
> I noticed that for our new Ilumina data (which generate Sanger format) the
> FastQ groomer output is identical to the Ilumina FastQ input file.
>
> I was hoping to go ahead and just use the raw FastQ files as input (saving
> disk space) for computing quality statistics to look at box plots, but it
> appears that the tool "Compute Quality Statistics" appears to require that
> the data have been run through FastQ Groomer first.
>
> Is there a way to get around this and is this a bug? I assuming this is some
> sort of safety measure built into this tool?
>
>  -John
>
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--
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
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