What are the recommended methods to call differential peaks for enrichment/pulldown datasets (e.g. MEDIPS, H3K4me3) of different conditions with many replicates?
- 20-30 biological replicates of condition1 pulldown+input pairs
- 20-30 biological replicates of condition2 pulldown+input pairs
- 20-30 biological replicates of condition3 pulldown+input pairs
So far I have seen the following:
- macs2 bdgdiff: for pairs of condition1 vs condition2 peaks called with macs2 callpeak https://github.com/taoliu/MACS/wiki/Call-differential-binding-events
This gives me the right output, e.g. regions enriched in condition1 vs condition2 and vice versa, as well as common.
The question is how do I combine my 20-30 biological replicates of condition1 and my 20-30 biological replicates of condition2 in macs2 bdg files to run the bdgdiff pairwise comparison mode?
THOR-2: seems to be able to do more than 2 in #rep1 and #rep2 lists http://www.regulatory-genomics.org/thor-2/tool-usage/
Other tools to investigate:
https://omictools.com/polyphemus-tool https://omictools.com/differential-identification-using-mixtures-ensemble-tool https://omictools.com/mmdiff-tool https://omictools.com/genome-wide-generalized-additive-model-tool https://omictools.com/normr-obeys-regime-mixture-rules-tool https://omictools.com/chromstar-tool
Other tools I discarded for this purpose:
- Segway, ChromHMM, ChromImpute: don't seem to have a differential mode.
- Epicode: differential mode seems to give differential "codes" as output, instead of regions (peaks).
- PARE: seems to call differential regions with no nucleosomes, rather than differential peaks.