Question: HOMER mergePeaks -d value definition
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gravatar for morovatunc
4.4 years ago by
morovatunc450
Turkey
morovatunc450 wrote:

Hi,

I would like understand definite physical meaning of d value. I am confused with 2 possible meanings. 

Could you tell me which one is true?

1)d is the bp value which accepts any overlap within that distance from the both ends of the peak.

ex1-> peak 1 > chr1 100 150

          peak 2  > chr1 70 90 

Based on this meaning if d is greater than 10, it takes peak 1 and peak 2 as an overlap. If not, it does not.

2)d is the bp value which accepts any overlap within that distance from the centre of the peak.

ex2 > peak 1 > chr1 100 150 ( centre is 125)

          peak 2 > chr1  70  110 (centre is 90)

Based on this meaning if d is greater than 35, it takes peak 1 and peak 2 as an overlap. If not, does not.

One last question:

Regardless from both of the physical meanings, If I set d to 100, regarding the both sides, does it take 100 bp from each side ? (which makes total 200) or 50 from each side ( which adds up to 100)

Dear santa if you are there, this will be the best xmas present ever. #BeMySanta...

Thank you.

Tunc

chip-seq homer • 1.3k views
ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by morovatunc450
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