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Old 03-24-2010, 08:56 AM   #1
bioenvisage
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Default number of contigs in velvet

hi all , what is the approximate total number of contigs we should get in a velvet assembly? I would like to know this because i did assemblies with various parameters but i always get more then million contigs..
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Old 03-24-2010, 11:05 AM   #2
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Use VelvetOptimizer.pl
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Old 03-24-2010, 11:27 AM   #3
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In a genomic assembly you should get exactly the number of chromosomes for that species or you've made a horrible mistake.

Seriously, i think you are beginning to shoot from the hip with your questions to this board. Post some more specifics or do some research on your own.
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Old 03-24-2010, 01:07 PM   #4
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What are you trying to assemble?

Here are some numbers from CLCbio tool: http://www.clcbio.com/index.php?id=1413

Lesser, longer contigs are better, provided they are not incorrect!
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Old 03-24-2010, 01:34 PM   #5
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hello zingster ..iam very new to this kind of research and iam not expertise like you in bioinfo ....so only i have these kind of questions araises..im sry if iam hard..
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Old 03-24-2010, 05:14 PM   #6
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This thread reminds me of something...thanks...(will post the idea in the Site Feedback forum shortly...)
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Old 03-24-2010, 08:10 PM   #7
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Default Searching in the dark

Yes, it's better we know the exact chr number. But not all the organisms we know their chromosome. A good way is to align to a closely related organism and then to check the left contigs.

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Originally Posted by Zigster View Post
In a genomic assembly you should get exactly the number of chromosomes for that species or you've made a horrible mistake.

Seriously, i think you are beginning to shoot from the hip with your questions to this board. Post some more specifics or do some research on your own.
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