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

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)

chip-seq
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written by prgrmmr70 • prgrmmr70

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

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written by rpolicastro rpolicastro

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

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written by prgrmmr70 • prgrmmr70

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

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written by rpolicastro 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.

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written by rpolicastro rpolicastro

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?

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updated by GenoMax GenoMax • written by prgrmmr70 • prgrmmr70

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

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written by rpolicastro rpolicastro

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

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written by prgrmmr70 • prgrmmr70

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

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written by rpolicastro rpolicastro

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