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Old 07-23-2010, 02:18 AM   #1
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 ?
syslm01 is offline   Reply With Quote
Old 07-23-2010, 03:20 AM   #2
Peter (Biopython etc)
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543

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.
maubp is offline   Reply With Quote

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