<div dir="ltr"><div dir="ltr" style="color:rgb(0,0,0);font-family:arial,sans-serif;font-size:13px">Hello Ken,<div><br></div><div>Did you install khmer from the master branch or the bleeding-edge branch?</div><div><br></div>
<div>Can you share with us the four complete command lines you executed?</div></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Aug 19, 2013 at 8:50 PM, Kenlee Nakasugi <span dir="ltr"><<a href="mailto:kenlee.nakasugi@sydney.edu.au" target="_blank">kenlee.nakasugi@sydney.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
<br>
I'm just starting to do some kmer-type analyses on my read data.<br>
I am trying to compare/find any differences in two different read datasets, and am trying to get some basic k-mer stats, but more importantly trying to figure out what would be the best type of comparison to do.<br>
<br>
I have already generated the hash (.kh) and hist (.hist) via the load-into-counting.py and abundance-dist.py scripts from khmer v0.4.<br>
Now from <a href="http://khmer.readthedocs.org/en/latest/blog-posts.html" target="_blank">http://khmer.readthedocs.org/en/latest/blog-posts.html</a> , i wanted to get the abundance by position, and hi-lo kmer distributions, but are the scripts listed there (and found in sandbox directory in khmer distribution) compatible with the output from 'load-into-counting.py and abundance-dist.py' ?<br>
<br>
I tried inputting the .hist and hash tables but getting errors like:<br>
<br>
##<br>
python /usr/local/bin/khmer/sandbox/abundance-hist-by-position.py R1.k32.hist<br>
... 0<br>
Traceback (most recent call last):<br>
File "/usr/local/bin/khmer/sandbox/abundance-hist-by-position.py", line 15, in <module><br>
countSum[i] += int(tok[i])<br>
ValueError: invalid literal for int() with base 10: '0.617'<br>
##<br>
<br>
Do I need to run these scripts from <a href="http://khmer.readthedocs.org/en/latest/blog-posts.html" target="_blank">http://khmer.readthedocs.org/en/latest/blog-posts.html</a> from scratch ?<br>
And any other types of comparisions useful?<br>
<br>
Any advice appreciated!<br>
<br>
Cheers,<br>
Ken<br>
_______________________________________________<br>
khmer mailing list<br>
<a href="mailto:khmer@lists.idyll.org">khmer@lists.idyll.org</a><br>
<a href="http://lists.idyll.org/listinfo/khmer" target="_blank">http://lists.idyll.org/listinfo/khmer</a><br>
</blockquote></div><br></div><br clear="all"><div><br></div>-- <br><div dir="ltr"><div style="font-size:small"><font face="courier new, monospace">Michael R. Crusoe Software Engineer <a href="mailto:mcrusoe@msu.edu" target="_blank">mcrusoe@msu.edu</a></font></div>
<div style="font-size:small"><font face="courier new, monospace"> @ the lab for Genomics, Evolution, and Development (GED)</font></div><div style="font-size:small"><font face="courier new, monospace"> home of the Khmer software suite </font><span style="font-family:'courier new',monospace"><a href="http://ged.msu.edu/" target="_blank">http://ged.msu.edu/</a></span></div>
</div>