<div dir="ltr"><br><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Feb 24, 2014 at 12:22 PM, Francesco Rubino [frr11] <span dir="ltr"><<a href="mailto:frr11@aber.ac.uk" target="_blank">frr11@aber.ac.uk</a>></span> wrote:<br>
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<p>Hi Michael,<br>
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<p>thanks for your reply. I wasn't sure about the version because I did find some documentation online about version 0.8.x and I got confused. Regarding the casava format, this is the page: <a href="http://khmer.readthedocs.org/en/latest/scripts.html" target="_blank">http://khmer.readthedocs.org/en/latest/scripts.html</a><br>
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<p>In the section about read handling it mention the format @name/1 as the latest.<br></p></div></div></blockquote><div><br></div><div>Thanks. I've updated this in the documentation for the newly released v0.8 of the khmer project.</div>
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<p>Should I change my files to be interleaved and with the headers in the old format (the one ending in /1 or /2) to make sure I </p>
<p>don't run into problems in some of khmer scripts?<br></p></div></div></blockquote><div><br></div><div>Correct. If you want your reads processed as pairs you need to use the /1,/2 format for now.</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<div style="color:#282828">I have code to interleave and detect the and convert the header format anyway, so it won't really be a problem, but I'd prefer not to if possible.</div></div></div></blockquote><div><br>
</div><div>Sorry, this is on our roadmap to fix this issue.</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div style="font-size:12pt;font-family:Calibri,Arial,Helvetica,sans-serif">
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<div>Thanks,<br>
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<div>Francesco<br>
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<div dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Michael R. Crusoe <<a href="mailto:mcrusoe@msu.edu" target="_blank">mcrusoe@msu.edu</a>><br>
<b>Sent:</b> 24 February 2014 17:07<br>
<b>To:</b> Francesco Rubino [frr11]<br>
<b>Cc:</b> <a href="mailto:khmer@lists.idyll.org" target="_blank">khmer@lists.idyll.org</a><br>
<b>Subject:</b> Re: [khmer] khmer/khmer-protocols confusion</font>
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<div class="gmail_quote">On Mon, Feb 24, 2014 at 10:58 AM, Francesco Rubino [frr11]
<span dir="ltr"><<a href="mailto:frr11@aber.ac.uk" target="_blank">frr11@aber.ac.uk</a>></span> wrote:<br>
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Hello all,</div>
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<div>Hello Francesco,</div>
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<div>Thank you for using the khmer suite and for your questions.</div>
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<div>I've read part of the documentation of khmer and I'm interested in using it to either partition or normalise a meta-transcriptome I have. I have a bit of confusion about the versions of the software, though. I have a few questions I hope you can answer:<br>
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<div>1) I've read both about a khmer 0.7.x (<a href="http://khmer.readthedocs.org/en/latest/" target="_blank">http://khmer.readthedocs.org/en/latest/</a>) and a 0.8.x (<a href="https://github.com/ctb/khmer/releases" target="_blank">https://github.com/ctb/khmer/releases</a>).
Which should I use?<br>
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<div>The official GitHub repository for khmer is <a href="https://github.com/ged-lab/khmer" target="_blank">
https://github.com/ged-lab/khmer</a>. The latest current release is v0.7.1. Our primary method for distribution is via the Python Package Index (
<a href="https://pypi.python.org/pypi/khmer" target="_blank">https://pypi.python.org/pypi/khmer</a> ) using the `pip` command as documented in <a href="http://khmer.readthedocs.org/en/latest/" target="_blank">http://khmer.readthedocs.org/en/latest/</a></div>
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<div>GitHub will present any branch or tag as a release. Titus's personal repository has a branch named "protocols-v0.8.3" in reference to the version of khmer-protocols not of the khmer project itself.</div>
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<div>2) I see in the documentation that you need to interleave the fastq files if using paired-end data. Why do you refer as "@name/1" as the new casava format? I thought that one is the old one.<br>
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<div>That would be our error. Supporting the new format is being tracked in this GitHub issue: <a href="https://github.com/ged-lab/khmer/issues/23" target="_blank">https://github.com/ged-lab/khmer/issues/23</a></div>
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<div>What document where you looking at?</div>
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<div>Thanks,<br>
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<div>Francesco Rubino<br>
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-- <br>
<div dir="ltr"><span style="font-family:'courier new',monospace;font-size:small">Michael R. Crusoe: Programmer & Bioinformatician </span><a href="mailto:mcrusoe@msu.edu" style="color:#1155cc;font-family:'courier new',monospace;font-size:small" target="_blank">mcrusoe@msu.edu</a><br style="font-family:'courier new',monospace;font-size:small">
<span style="font-family:'courier new',monospace;font-size:small"> @ the Genomics, Evolution, and Development lab; Michigan State U</span><br style="font-family:'courier new',monospace;font-size:small">
<a href="http://ged.msu.edu/" style="color:#1155cc;font-family:'courier new',monospace;font-size:small" target="_blank">http://ged.msu.edu/</a><span style="font-family:'courier new',monospace;font-size:small"> </span><a href="http://orcid.org/0000-0002-2961-9670" style="color:#1155cc;font-family:'courier new',monospace;font-size:small" target="_blank">http://orcid.org/0000-0002-2961-9670</a><span style="font-family:'courier new',monospace;font-size:small"> </span><a href="http://twitter.com/biocrusoe" style="color:#1155cc;font-family:'courier new',monospace;font-size:small" target="_blank">@biocrusoe</a><br>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr"><span style="font-family:'courier new',monospace;font-size:small">Michael R. Crusoe: Programmer & Bioinformatician </span><a href="mailto:mcrusoe@msu.edu" style="color:rgb(17,85,204);font-family:'courier new',monospace;font-size:small" target="_blank">mcrusoe@msu.edu</a><br style="font-family:'courier new',monospace;font-size:small">
<span style="font-family:'courier new',monospace;font-size:small"> @ the Genomics, Evolution, and Development lab; Michigan State U</span><br style="font-family:'courier new',monospace;font-size:small"><a href="http://ged.msu.edu/" style="color:rgb(17,85,204);font-family:'courier new',monospace;font-size:small" target="_blank">http://ged.msu.edu/</a><span style="font-family:'courier new',monospace;font-size:small"> </span><a href="http://orcid.org/0000-0002-2961-9670" style="color:rgb(17,85,204);font-family:'courier new',monospace;font-size:small" target="_blank">http://orcid.org/0000-0002-2961-9670</a><span style="font-family:'courier new',monospace;font-size:small"> </span><a href="http://twitter.com/biocrusoe" style="color:rgb(17,85,204);font-family:'courier new',monospace;font-size:small" target="_blank">@biocrusoe</a><br>
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