<div dir="ltr">My reading of the code is that they're trimmed from the end and so I think you should be able to write the script without too much difficulty. (Sorry for the inconvenience - we'll hopefully have the necessary changes in khmer in the next month or two.)<div>
<br></div><div style>For suggestions about assemblers, I know that there are people on this list who are much better qualified than I am to answer that question. I _hope_ that one or more of them will speak up. I just CC'd two of them in an attempt to prod them into participating in this thread. (My background is in physics and high performance computing, not in biology. I've been teaching myself some things about bioinformatics during the 1.25 years I've worked at this job, but I still don't have much exposure to bioinformatics tools outside of khmer and screed. :-)</div>
</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Apr 11, 2013 at 3:05 AM, Jens-Konrad Preem <span dir="ltr"><<a href="mailto:jpreem@ut.ee" target="_blank">jpreem@ut.ee</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
I eagerly wait for such functionality, right now I'm in a bit of a
hurry. Maybe if I have some more free time I can decipher the "below
-abund" and screed codes eneact my own changes in it if so I'll post
it. Right now I've made a Perl script (slowish though) to gather the
scores from keep and give those to names/seqs of keep.below - if
they're trimmed then I' of course in trouble again, are they trimmed
in some specific way from ends or something, then it might not be
too hard to add this trimming function to my script to make the
scores to correspond to sequence.<br>
<br>
In case I fail in my task, have you any suggestions for paired end
assemblers that don't take quality scores+ I've tried Cope but for
some reason it produced very little alignments. (Compared to flash
for example) - I'd like to merge the normalized (and hopefully
partitioned) pairs before assembly6 with the likes of velvet or
SoapDenovo. If all goes sideways what are your thoughts on - a)
assembly without merging pairs, b) merging pairs (with Flash etc.)
before any modification by khmer (normalisation,parititioning).<br>
<br>
Jens-Konrad<div><div class="h5"><br>
<br>
<div>On 04/11/2013 03:08 AM, Eric McDonald
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">I believe that the 'filter-below-abund.py' script
trims sequences. So, your Perl script may need to also truncate
the quality scores line down to the length of the trimmed
sequences.
<div><br>
</div>
<div>
By the way, we are working on getting the scripts to output
FASTQ if they receive FASTQ inputs, but that functionality is
not ready yet. You're definitely not the only person
interested in that functionality. ;-)</div>
<div><br>
</div>
<div>Hope that helps,</div>
<div> Eric</div>
<div><br>
</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Wed, Apr 10, 2013 at 8:13 AM,
Jens-Konrad Preem <span dir="ltr"><<a href="mailto:jpreem@ut.ee" target="_blank">jpreem@ut.ee</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
I have just a quick question. Filter-below-abund takes a
fastq file and outputs a fasta file.<br>
Can I make use of a Perl script that would take the names
from the resulting file and add the quality scores from the
previous file. As I understand nothing happens to the names
or sequences - some of them just get culled.<br>
<br>
I want to try out the normalized data with some paired end
reads assemblers that use quality scores/fastq files.<br>
I think its easier for me to write such Perl script than to
modify filter-below-abund.py to output fastq.<br>
<br>
Not much of a python guy - though it seems that there
shouldn't be too much work on replacing screed.fasta with
screed.fastq etc., but I find it is quite often easier to
write a few lines than to parse what someone else wrote and
why and then try to modify it :D.<br>
<br>
Jens-Konrad Preem, MSc., University of Tartu<br>
<br>
<br>
<br>
<br>
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</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
<div dir="ltr">
<div>Eric McDonald</div>
<div>HPC/Cloud Software Engineer</div>
<div> for the Institute for Cyber-Enabled Research (iCER)</div>
<div> and the Laboratory for Genomics, Evolution, and
Development (GED)</div>
<div>Michigan State University</div>
<div>P: <a href="tel:517-355-8733" value="+15173558733" target="_blank">517-355-8733</a></div>
</div>
</div>
</blockquote>
<br>
</div></div><span class="HOEnZb"><font color="#888888"><pre cols="72">--
Jens-Konrad Preem, MSc, University of Tartu</pre>
</font></span></div>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr"><div>Eric McDonald</div><div>HPC/Cloud Software Engineer</div><div> for the Institute for Cyber-Enabled Research (iCER)</div><div> and the Laboratory for Genomics, Evolution, and Development (GED)</div>
<div>Michigan State University</div><div>P: 517-355-8733</div></div>
</div>