How to test statistical significance of ChIPseq enrichment in custom BED regions?

Question

[AlexAbdulkaderKheirallah]

Hello All,

Say I have a list of regions in BED format + list of ChIPseq peaks in BED format or ChIPseq BAM alignment file. How can I statistically test that factor's occupancy is enriched in BED regions more than would be expected by chance? Is there any specific program I could use for that purpose? Thus far I relied on ngs.plot to draw enrichment over various custom BED regions but I want to show that these enrichment are statistically significant.

Thanks

Answer 1

[Fidel]

I think this previous answer is what you are looking for: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. genome average)

[AlexAbdulkaderKheirallah]

Thanks I think I will settle with GenometriCorr for good data visualization functionality.

Answer 2

[Ian]

You could try using the Genomic Hyperbrowser (an instance of Galaxy) where you can pose the same question. You upload your data as different "tracks" and then ask whether there is significant coverage (one option).

I advise you check out the tutorial video first.