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Hi,<br>
<br>
Finally I went through the problems I was facing.<br>
I changed the kmer value from 20 to the default (32) and all works
perfectly.<br>
Now waiting for the result of the assembly and the benchmark with or
without khmer treatments<br>
<br>
Thanks again for all your help and your work<br>
<br>
Alexis<br>
<br>
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.<br>
<br>
<div class="moz-cite-prefix">Le 22/03/2013 06:27, C. Titus Brown a
écrit :<br>
</div>
<blockquote cite="mid:20130322052737.GF29874@idyll.org" type="cite">
<pre wrap="">On Thu, Mar 21, 2013 at 04:51:30PM +0100, Alexis Groppi wrote:
</pre>
<blockquote type="cite">
<pre wrap="">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)
</pre>
</blockquote>
<pre wrap="">
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
<a class="moz-txt-link-freetext" href="http://arxiv.org/abs/1212.0159">http://arxiv.org/abs/1212.0159</a>
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
</pre>
</blockquote>
<br>
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