Q: the questions about calling broad peaks

[liuyu988]

Hi, i want to call broad peaks for histone mark H3K27me3. but i am confused with the infomation about the broad parameters.

(1) In my opinion, i think this four parameters are important for calling broad peaks:

      - --max-gap 
      - --min-length 
      - --broad   
      - --broad-cutoff 

Maybe you can tell me some other parameters I'm ignoring?

(2) and i noticed The maximum gap is expanded to 4 * MAXGAP (--max-gap parameter).

so if i want to merge the peaks within 1000bp, i will set the --max-gap is 250. could you tell me if this's right?

(3) and for my understanding: The bigger max-gap parameter will merge peaks within a bigger distance into one peak; so the bigger max-gap is , the fewer peaks there are. But in my test, there maybe a opposite trend in many times, exspecially in some small max-gap, such as: 250,375,500... ; for example:

the number of peaks | max-gap

• 107705 | 250
• 110317 | 500
• 110558 | 750

(4)and the default of max-gap parameter is read length/tag size. I wonder if I set a value smaller than the fragment size, it will cause any wrong effects?

could anyone can help me? thanks a lot!!
YU