[khmer] abundance-dist for paired end data

[C. Titus Brown]

There is no good way at the moment to give multiple sequence files to
abundance-dist, sorry :(.  You might be able to combine sample.hist files
afterwards... hmm.  But for now, I think interleaving is the best option,
as Chris says.

best,
--titus

On Wed, Oct 16, 2013 at 09:02:50PM +0000, Fields, Christopher J wrote:
> Personally, I interleave the reads and run them together for all the analyses, then split them later (after filtering, etc).  But it would be interesting to hear of other options?
> 
> chris
> 
> On Oct 16, 2013, at 3:54 PM, Nacho Caballero <nachocab at gmail.com<mailto:nachocab at gmail.com>>
>  wrote:
> 
> 
> I?m following the STAMPS tutorial<http://ged.msu.edu/angus/2013-hmp-assembly-webinar/exploring-stamps-data.html> and I created the bloom filter for my two paired end files
> 
> python load-into-counting.py -x 1e8 -k 20 sample.kh<http://sample.kh/> sample_1.fastq sample_2.fastq
> 
> Now I?m trying to generate the distribution, but there is no -p option, how should I do it?
> 
> python abundance-dist.py sample.kh<http://sample.kh/> ??.fastq sample.hist
> 
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-- 
C. Titus Brown, ctb at msu.edu