[khmer] [cy_jiang at 126.com: Questions about digital normalization]

[C. Titus Brown]

----- Forwarded message from cy_jiang <cy_jiang at 126.com> -----

Date: Sat, 13 Jul 2013 10:24:09 +0800 (CST)
From: cy_jiang <cy_jiang at 126.com>
To: ctb at msu.edu
Subject: Questions about digital normalization
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 Hello Professor C. Titus Brown,

I am trying to implement digital normalization on paired-end reads and now I have some questions regarding the usage of it. Would you kind enough to help me out of them? Since I am new in bioinformatics, please spare me if I am not able to put it clearly.

I got forward and reverse reads in two different FASTA files. Each of them contains 16 million reads of length 100bp (a total of 32m reads). I would like to diginorm them and then assemble them using Velvet and Oases. I saw the example you give out here (https://khmer.readthedocs.org/en/latest/scripts.html) and found only one file (test-abund-read-paired.fa) in the example. Does this file contain all the paired-end reads? If it is the case, is there any format criteria for it (like each read is next to its mate read)?  

What is more, I am curious about how the normalization works when provided with paired-end reads. I was thinking to join mate reads together into a sequence of 200bp (16m reads of length 200 in a file). According to the paper you published, digital normalization discards or accepts the whole sequence, and this promises me no orphan reads left. But this will of course increase the kmer number, which results in more RAM. Since I only got a 16GB RAM, I am afraid that there may not enough RAM for this solution. What should I set for the parameters -N and -x?

Would you please explain how diginorm deals with paired-end reads and recommend a better solution for my case?
Looking forword to your reply!

Best regards!

Daniel
----- End forwarded message -----

-- 
C. Titus Brown, ctb at msu.edu