<p>I have ChIP-seq data with peaks called by MACS in peaks.bed and summits.bed files. From here I would like to visualise the peaks on either the IGV or UCSC&#39; Genome Browser. I understand that the bed files give me the positions and size of the peaks called by MACS, but how do I actually visualise the height / distribution of the peaks? Do I have to get the genome coverage for each base from my bam file, then filter for peak regions listed in the bed files, and then convert to a bedgraph, wig, or bigwig format?</p>

1\. Use `-w` and `-S` parameters, which gives you two 'wig' files: One for Control and another for TREATMENT. Wiggle (wig) file gives you the distribution and coverage (height) of peaks which you can upload on UCSC or IGV . Read more about the other parameters [here][1].

---Example:

    macs14 -c <CONTROL_FILE> -t <TREATMENT_FILE> -n OUTPUT_NAME -f BAM -g hs -w -S

<img alt="MACS peaks" src="http://bioinformatics.kandurilab.org/biostars/MACS_wiggle_example.png" style="height:51px; width:300px" />

2\. If you want to just show the coverage over predicted peak regions by MACS, use BEDtools to extract only the portion of 'wig' file overlapping with peak regions (BED file).

 [1]: https://github.com/taoliu/MACS/blob/macs_v1/README.rst