About the read depth of coverage

El Mariachi · 11-29-2010, 07:11 PM

Hello,

I am a beginner. I want to find all the copy number variations

in the genome of pig by the Illumina/Solexa Squencing but I do not

know what the coverage will be proper---20x, 10x, 5x, 1x, or smaller?

If the coverage is too high, the cost will also increase too much.

Thanks in advance.

drio · 11-30-2010, 04:50 AM

Take a look to the CNV analysis tools in the wiki. Some of them have publications
associated. You'll see they work with pretty low coverage.

El Mariachi · 12-30-2010, 12:22 AM

Quote:

Originally Posted by drio

Take a look to the CNV analysis tools in the wiki. Some of them have publications
associated. You'll see they work with pretty low coverage.

Thank you for your suggestion, I am going to have a try between 1x and 4x.

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11-29-2010, 07:11 PM	#1
El Mariachi Junior Member Location: China Join Date: Feb 2010 Posts: 4	About the read depth of coverage Hello, I am a beginner. I want to find all the copy number variations in the genome of pig by the Illumina/Solexa Squencing but I do not know what the coverage will be proper---20x, 10x, 5x, 1x, or smaller? If the coverage is too high, the cost will also increase too much. Thanks in advance. Last edited by El Mariachi; 11-29-2010 at 07:14 PM.

11-30-2010, 04:50 AM	#2
drio Senior Member Location: 41°17'49"N / 2°4'42"E Join Date: Oct 2008 Posts: 323	Take a look to the CNV analysis tools in the wiki. Some of them have publications associated. You'll see they work with pretty low coverage. __________________ -drd