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Old 10-15-2010, 04:08 AM   #1
oliviera
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Default coverage required

Dear all,

I try to get an idea of the base coverage required for the different sequencing applications.
I didn t find any review on this subject so if you know a nice paper or can complete the followings, your are more than welcome:

- whole genome resequencing: 40x genome size (Nature 464, 587-591)
- SNPs call: 31x genome size (Genome Res. 2010. 20: 273-280)
- de novo genome modelling: 100x ??
- de novo transcriptome modelling: 100x??
- transcript expression studies: ??


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Old 10-15-2010, 10:21 AM   #2
malachig
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The relationship between library depth and transcript expression profiling is discussed at some length in the supplementary materials of Nature Methods. 2010 Oct;7(10):843-847 (ALEXA-Seq).

The Trans-ABySS manuscript provides an example of de novo transcriptome assembly that might be helpful.
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Old 10-17-2010, 11:40 PM   #3
francois.sabot
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Quote:
Originally Posted by oliviera View Post

- whole genome resequencing: 40x genome size (Nature 464, 587-591)
This amount of 'x' depend also of the size of your reads: longer reads need less coverage for the same efficiency
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