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Old 07-23-2010, 02:18 AM   #1
syslm01
Member
 
Location: china

Join Date: Apr 2010
Posts: 16
Default coverage file

Hi all,

I use tophat to analyze one dataset with 27bp length, and I am confused about the coverage.wig file it generated.

Here is one example:

chr1 11116146 11116147 47
chr1 11116147 11116149 45
chr1 11116149 11116150 42
chr1 11116150 11116151 40
chr1 11116151 11116152 5
chr1 11116152 11116154 4
chr1 11116154 11116657 0
chr1 11116657 11116658 3
chr1 11116658 11116659 4

Does the third column stand for the number of reads that cover the site ?
So does it mean there are 47 reads in 11116147 and 11116146 respectively ?
But my reads is only 27bp, so the max number of reads coverage at one site should be < 27, I am confused why there are some sites that the number of reads coverage is > 27.

Does anyone have some ideas ?
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Old 07-23-2010, 03:20 AM   #2
maubp
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Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543
Default

If you have a million reads, your coverage values will be in the range from 0 (for regions with no coverage) to a possible maximum of one million deep (if you are unlucky and all your reads map in one place).

The fact that your reads are just 27bp long doesn't matter here.
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