<div dir="ltr">Hi Mamoon,<div>What kind of assembly would you be talking about? </div><div><br><div>Protocols for mRNAseq and metagenomics here: <a href="https://khmer-protocols.readthedocs.org/en/v0.8-1/index.html">https://khmer-protocols.readthedocs.org/en/v0.8-1/index.html</a></div>
<div><br></div><div>I found the mRNAseq protocol pretty straight-forward.</div><div><br></div><div>-John</div><div><br></div><div><br></div></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Nov 5, 2013 at 5:54 AM, <span dir="ltr"><<a href="mailto:khmer-request@lists.idyll.org" target="_blank">khmer-request@lists.idyll.org</a>></span> wrote:<br>
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1. Using khmer on paired-end Illumina data set (Mamoon Rashid)<br>
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Message: 1<br>
Date: Tue, 5 Nov 2013 13:53:52 +0300<br>
From: Mamoon Rashid <<a href="mailto:rashidmamoon@gmail.com">rashidmamoon@gmail.com</a>><br>
Subject: [khmer] Using khmer on paired-end Illumina data set<br>
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Dear khmer users,<br>
Please let me know the easy way to reduce my dataset (13.9 m PE reads)<br>
which shows a lot of duplicates in the FastQC plots (attached). This<br>
resulted into very fragmented assembly using velvet.<br>
Any suggestions are most welcome.<br>
Best regards<br>
Mamoon<br>
<br>
<br>
--<br>
*Mamoon Rashid, PhD*<br>
Post-Doctoral Fellow<br>
Marine Microbial Ecology Lab<br>
Red Sea Research Center<br>
4700 King Abdullah University of Science and Technology (KAUST)<br>
Room 2217-WS03, Ibn Al-Haytham Building (2)<br>
4700 *King* *Abdullah* *University* *of* *Science* *and* *Technology*<br>
Thuwal 23955-6900, Kingdom of Saudi Arabia<br>
Office: <a href="tel:%2B966%20%280%29%202%20808-2671" value="+96628082671">+966 (0) 2 808-2671</a><br>
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End of khmer Digest, Vol 10, Issue 1<br>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr"><div><span style="color:rgb(102,102,102)">Postdoctoral Research Associate</span><br></div><div><span style="background-color:rgb(255,255,255)"><font color="#666666">Department of Biology, University of Vermont</font></span></div>
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