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Hi,
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<div>I have a few more questions, specifically about the abundance-dist.py. I used load load-into-counting.py to make an hash table, but why abundance-dist.py doesn't support multiple files?</div>
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<div>If I run abundance-dist.py on a per-file base and concatenate the .hist files, will I get the same results, or should I concatenate all my sequence file into one to get the overall histogram for my dataset?</div>
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<div>Thanks for your help,</div>
<div>Francesco</div>
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<div>On 28 Feb 2014, at 20:43, Michael R. Crusoe <<a href="mailto:mcrusoe@msu.edu">mcrusoe@msu.edu</a>> wrote:</div>
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On Mon, Feb 24, 2014 at 12:22 PM, Francesco Rubino [frr11]<span class="Apple-converted-space"> </span><span dir="ltr"><<a href="mailto:frr11@aber.ac.uk" target="_blank">frr11@aber.ac.uk</a>></span><span class="Apple-converted-space"> </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>
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<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>
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<div>Correct. If you want your reads processed as pairs you need to use the /1,/2 format for now.</div>
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<div style="color: rgb(40, 40, 40);">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>
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<div>Sorry, this is on our roadmap to fix this issue.</div>
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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" style="font-size: 11pt;"><b>From:</b><span class="Apple-converted-space"> </span>Michael R. Crusoe <<a href="mailto:mcrusoe@msu.edu" target="_blank">mcrusoe@msu.edu</a>><br>
<b>Sent:</b><span class="Apple-converted-space"> </span>24 February 2014 17:07<br>
<b>To:</b><span class="Apple-converted-space"> </span>Francesco Rubino [frr11]<br>
<b>Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:khmer@lists.idyll.org" target="_blank">khmer@lists.idyll.org</a><br>
<b>Subject:</b><span class="Apple-converted-space"> </span>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 class="Apple-converted-space"> </span><span dir="ltr"><<a href="mailto:frr11@aber.ac.uk" target="_blank">frr11@aber.ac.uk</a>></span><span class="Apple-converted-space"> </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<span class="Apple-converted-space"> </span><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 (<span class="Apple-converted-space"> </span><a href="https://pypi.python.org/pypi/khmer" target="_blank">https://pypi.python.org/pypi/khmer</a><span class="Apple-converted-space"> </span>) 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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--<span class="Apple-converted-space"> </span><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" target="_blank" style="color: rgb(17, 85, 204); font-family: 'courier new', monospace; font-size: small;">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/" target="_blank" style="color: rgb(17, 85, 204); font-family: 'courier new', monospace; font-size: small;">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" target="_blank" style="color: rgb(17, 85, 204); font-family: 'courier new', monospace; font-size: small;">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" target="_blank" style="color: rgb(17, 85, 204); font-family: 'courier new', monospace; font-size: small;">@biocrusoe</a><br>
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<span style="font-family: 'courier new', monospace; font-size: small;">Michael R. Crusoe: Programmer & Bioinformatician </span><a href="mailto:mcrusoe@msu.edu" target="_blank" style="color: rgb(17, 85, 204); font-family: 'courier new', monospace; font-size: small;">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/" target="_blank" style="color: rgb(17, 85, 204); font-family: 'courier new', monospace; font-size: small;">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" target="_blank" style="color: rgb(17, 85, 204); font-family: 'courier new', monospace; font-size: small;">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" target="_blank" style="color: rgb(17, 85, 204); font-family: 'courier new', monospace; font-size: small;">@biocrusoe</a></div>
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