[khmer] abundance-dist for paired end data

Fields, Christopher J cjfields at illinois.edu
Wed Oct 16 14:02:50 PDT 2013

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…


On Oct 16, 2013, at 3:54 PM, Nacho Caballero <nachocab at gmail.com<mailto:nachocab at gmail.com>>

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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