The maximum number of peaks in a ChIP-seq data (bigWig format)

Question

[prgrmmr70]

How we can find the maximum number of peaks (coverage) in a bigWig data file to analyze a chip-seq data?
I do not know if the following command from HOMER can do it for me. Cuz I am new in ChIp-seq analysis and Tools for analysis. -wig <wiggle file="" 1=""> [wiggle file 2] ... (read coverage counts from wiggle files)

[rpolicastro]

Can you expand more on what you mean by maximum number of peaks?

[prgrmmr70]

I mean the number of binding sites in the background (control/mock samples against treatment ) in which we can find enriched peaks (which are specific to the type of target protein) using peak calling tools. The enriched peaks are a subset of maximum number of peaks in background data

[rpolicastro]

Do you have the SAM/BAM file that was used to generate the bigWig?

[prgrmmr70]

I download bigWig file from the following link and it seems that there are bam file as well:

https://genome.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeBroadHistone

[rpolicastro]

The broadPeak files are the ones that will have the actual peaks. If you count the number of rows that corresponds to the number of called peaks.

[prgrmmr70]

I downloaded broadPeak file and opened it in a text editor. the rows are as follows:

chr1 237626 238382 . 538 . 11.582263 15.7 -1

chr1    237630  237993  .   883 .   24.121738   100.0   -1

chr1    521468  521696  .   560 .   12.388499   7.6 -1

chr1    567497  567683  .   532 .   11.389426   3.6 -1

chr1    569802  570042  .   640 .   15.299796   14.0    -1

chr1    713940  714346  .   468 .   9.044214    8.8 -1

chr1    793443  793633  .   526 .   11.149649   3.5 -1

chr1    804826  805736  .   620 .   14.588478   15.7    -1

You mean the number of rows like the above example?

[rpolicastro]

Yep, since each row is a peak it's as simple as counting the number of rows.

[prgrmmr70]

Is it the output file after peak calling? for example using MACS?

[rpolicastro]

You'll need to check the documentation for the exact peak caller they used, but that is from a peak caller.