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 <ozborn@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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