[khmer] Duration of do-partition.py (very long !) (Alexis Groppi)

Alexis Groppi alexis.groppi at u-bordeaux2.fr
Wed Apr 3 02:38:33 PDT 2013


Hi,

Finally I went through the problems I was facing.
I changed the kmer value from 20 to the default (32) and all works 
perfectly.
Now waiting for the result of the assembly and the benchmark with or 
without khmer treatments

Thanks again for all your help and your work

Alexis

PS : I'm using the "bleeding-edge" version of khmer. I found a lot a 
very useful extra scripts in the "sandbox directory" but it lacks a 
Readme file with a very short description of each of them.

Le 22/03/2013 06:27, C. Titus Brown a écrit :
> On Thu, Mar 21, 2013 at 04:51:30PM +0100, Alexis Groppi wrote:
>> Sorry for bothering you, but it's not clear for me :
>>
>> For removing the artefacts :
>> Should I apply find-knots on my file.below ? (after
>> normalize-by-median.py, load-into-counting.py and filter-below-abund.py)
>> Then filter-stoptags ?
>> And then will I have data ready for assembly or should I perform
>> do-partition.py ? (on these artefact free data)
> Good questions -- it's hard to figure out how to convey this stuff
> when we don't entirely understand what's going on in the first place
> with the artifacts (see
>
> http://arxiv.org/abs/1212.0159
>
> for our best guess).
>
> Start with your data after filter-below-abund.  Then apply
>
> ---
>
> python scripts/load-graph.py -x 8e9 lump corn-50m.lump.fa
>
> python scripts/make-initial-stoptags.py lump
>
> python scripts/partition-graph.py --stoptags lump.stoptags lump
>
> python scripts/find-knots.py -x 2e8 -N 4 lump
>
> python scripts/filter-stoptags.py *.stoptags corn-50m.lump.fa
>
> ---
>
> and follow with applying straight-up partitioning to the stopfilt
> file.
>
> best,
> --titus
>

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