[mira_talk] Re: megahubs in MIRA

Hi Isabelle,
Out of so many precious and experienced members of this talk-list, i should not 
be advising, but i ran into same problem before. 
how did you get rid of contamination? i am asking this because, it took me some 
time to figure out the solution, that was giving me hard time with my data..
just after that, i mean when one is fully confident of preprocess, you can set 
allowed megahub ratio with -AS:mmhr= integer . you can see the ratio you are 
facing in the very same complain of mira..
Best,Visam..

Date: Tue, 20 Mar 2012 14:36:58 +0100
Subject: [mira_talk] megahubs in MIRA
From: isabelle.lesur.kupin@xxxxxxxxx
To: mira_talk@xxxxxxxxxxxxx

Hello,

I am trying to perform an assembly consisting of 84 086 Sanger reads with 
qualities.

I used the following command:

-bash-3.2$ mira --project=OCV2_prime_full_length 
--job=denovo,genome,normal,sanger --noclipping=all --notraceinfo SANGER_SETTINGS


And the assembly stopped bacause of Megahubs.
Total megahubs: 8

I followed the recommandations MIRA gave me:
- I checked for vector/adaptor sequences
- I set the -SK:nrr parameter as follow: 
-SK:nrr=10 and -SK:nrr=20 and -SK:nrr=30

The number of megahubs reached 66 with the -SK:nrr parameter
- I used the -SK:mmhr parameter
This time, the number of megahubs reached 74

I then used RepeatMasker to mask the repeats in my sequenced and clipped all 
the Ns.

This time, I ended up with 66 megahubs....

So, does anybody know how I could get read off these megahubs???


Thank you for your help!

Isabelle

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