[khmer] khmer Digest, Vol 10, Issue 1

[John Stanton-Geddes]

Hi Mamoon,
What kind of assembly would you be talking about?

Protocols for mRNAseq and metagenomics here:
https://khmer-protocols.readthedocs.org/en/v0.8-1/index.html

I found the mRNAseq protocol pretty straight-forward.

-John




On Tue, Nov 5, 2013 at 5:54 AM, <khmer-request at lists.idyll.org> wrote:

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>    1. Using khmer on paired-end Illumina data set (Mamoon Rashid)
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> Message: 1
> Date: Tue, 5 Nov 2013 13:53:52 +0300
> From: Mamoon Rashid <rashidmamoon at gmail.com>
> Subject: [khmer] Using khmer on paired-end Illumina data set
> To: khmer at lists.idyll.org
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> AaXmzWwOE9aWC+E2-CX3nyxOyQ at mail.gmail.com>
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>
> Dear khmer users,
> Please let me know the easy way to reduce my dataset (13.9 m PE reads)
> which shows a lot of duplicates in the FastQC plots (attached). This
> resulted into very fragmented assembly using velvet.
> Any suggestions are most welcome.
> Best regards
> Mamoon
>
>
> --
> *Mamoon Rashid, PhD*
> Post-Doctoral Fellow
> Marine Microbial Ecology Lab
> Red Sea Research Center
> 4700 King Abdullah University of Science and Technology (KAUST)
> Room 2217-WS03, Ibn Al-Haytham Building (2)
> 4700 *King* *Abdullah* *University* *of* *Science* *and* *Technology*
> Thuwal 23955-6900, Kingdom of Saudi Arabia
> Office: +966 (0) 2 808-2671
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-- 
Postdoctoral Research Associate
Department of Biology, University of Vermont
Room 211, Marsh Life Science Building
109 Carrigan Drive
Burlington, Vermont 05405
www.johnstantongeddes.org
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