Question: Calling differential peaks on large set of 3 conditions
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22 months ago by
United Kingdom
141341254653464453.4k wrote:

Hi all,

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:

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?

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.

Thanks

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