[khmer] Use diginorm to delete identical reads

[C. Titus Brown]

Exactly!

Err, although I have to ask -- why are you trying to do diginorm
on reads of length 100 bp with k=100?  Is this an attempt to remove
artificially duplicated sequences?

cheers,
--titus

On Mon, Aug 05, 2013 at 09:24:37AM +0200, Karl Nordstr?m wrote:
> Hi Daniel,
> 
> I had the same error recently and learned that the maximum boundary of for
> khmer is 32. I was told that a relaxation of this limitation is in the
> pipeline.
> 
> Best,
> 
> Karl
> 
> 
> On Mon, Aug 5, 2013 at 8:38 AM, cy_jiang <cy_jiang at 126.com> wrote:
> 
> > Hi all,
> >
> > I am wondering if I can use diginorm to remove identical reads from my
> > dataset.* *
> > *
> > *
> > Precisely, I got paired-end reads of length 100bp. I first interleaved the
> > reads into one file, then ran diginorm with -k 100 -C 1 -x 7.2e9 -N 4. Then
> > the following information prompted up:
> > python: ktable.cc:21: khmer::HashIntoType khmer::_hash(const char*,
> > khmer::WordLength, khmer::HashIntoType&, khmer::HashIntoType&): Assertion
> > `k <= sizeof(HashIntoType)*4' failed.
> > What did this exactly mean? Is there anything I can do to achieve the
> > goal?
> >
> > Thanks in advance!
> >
> > Daniel
> >
> > _______________________________________________
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> > khmer at lists.idyll.org
> > http://lists.idyll.org/listinfo/khmer
> >
> >

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