HOMER mergePeaks -d value definition
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8.6 years ago
morovatunc ▴ 560

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)

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Thank you.

Tunc

ChIP-Seq HOMER • 2.4k views