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 > > ___________________________________________________________ > 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 > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > -- 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 using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/