HOMER mergePeaks -d value definition
0
0
Entering edit mode
8.2 years ago
morovatunc ▴ 550

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 • 2.3k views
ADD COMMENT

Login before adding your answer.

Traffic: 2305 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6