sparse peak calling

Question

[kanwarjag]

I have a Chipseq data and I expects peaks should be sparse. Which tool may be best to call sparse peaks? Can I also use same tool for calling sparse peaks of cut and Run experiment.

Thanks

[rpolicastro]

Do you mind defining what you consider sparse peaks?

[kanwarjag]

The low read depths and background levels and broader peaks.

[Morris_Chair]

Hi Kanwarjag, why don't you increase the depth of sequencing ? or merge more IP

Answer 1

[AS]

You can try SEACR : https://epigeneticsandchromatin.biomedcentral.com/articles/10.1186/s13072-019-0287-4