[khmer] diginorm on merged reads

[C. Titus Brown]

Hmm, more later, but on merged reads should be fine.  Should result in
same outcome as -p and then merging the reads.

cheers,
--titus

On Fri, Jul 26, 2013 at 04:10:36PM -0400, John Stanton-Geddes wrote:
> Hi Titus and the khmer list,
> I'm working on transcriptome assembly with samples treated at 12 different
> temperatures to capture genes expressed across the thermal range of my
> favorite ant species. I pooled the samples and ran them in a single lane of
> 100 bp paired end HiSeq, so I have about 16 million reads per sample, 160
> million reads total.
> 
> My question:
> is there any benefit to merging my paired-end reads (e.g. using FLASH
> http://bioinformatics.oxfordjournals.org/content/early/2011/09/07/bioinformatics.btr507)
> prior to running diginorm? A preliminary run of FLASH on some of my samples
> showed that about 65% of reads are merged (which is a bit surprising since
> the library was supposed to have been size-selected at 200 bp).
> 
> My thought is to run diginorm on the merged reads, and also on the
> un-merged reads using the `-p` option as documented previously (
> http://lists.idyll.org/pipermail/khmer/2013-July/000123.html). I'd then
> combine all these and run a second pass of diginorm.
> 
> Is this a valid approach, or is merging reads redundant with what diginorm
> does (since reads that add extra coverage would be tossed out anyway)?
> 
> Apologies if this is a noob question.
> 
> Thanks for the software!
> 
> -John
> 
> -- 
> Postdoctoral Research Associate
> Department of Biology, University of Vermont
> Room 211, Marsh Life Science Building
> 109 Carrigan Drive
> Burlington, Vermont 05405
> www.johnstantongeddes.org

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-- 
C. Titus Brown, ctb at msu.edu