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macs3-project / MACS

MACS -- Model-based Analysis of ChIP-Seq
https://macs3-project.github.io/MACS/
BSD 3-Clause "New" or "Revised" License
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fold enrichment #259

Open wangjiawen2013 opened 5 years ago

wangjiawen2013 commented 5 years ago

When building signal track with MACS2, the FE signal in genome range where the coverage is very low will become very significant, because the denominator is near zero in that range. Could you assign a weight to the low coverage range to avoid this artifact ?

wangjiawen2013 commented 5 years ago

And, can I build signal track to obtain FE signal without --SPMR ?

wangjiawen2013 commented 5 years ago

When building signal track with MACS2, the FE signal in genome range where the coverage is very low will become very significant, because the denominator is near zero in that range. Could you assign a weight to the low coverage range to avoid this artifact ?

Sorry, logLR signal has already done that.

taoliu commented 5 years ago

When building signal tracks, if you used 'bdgcmp' command, you can assign a bigger pseudocount to overcome such issue -- "-p PSEUDOCOUNT".

YiqunCao commented 5 years ago

I have my own bedGraph files for control and treatment. There are zeros in control file and I would like to generate ppois signal track (-m ppois). So I applied "-p PSEUDOCOUNT" and tried a few pseudocount 0.00001, 0.05, 0.1... But none of them actually works. The following error always appears: Exception AssertionError: 'Lambda must > 0, however we got 0' in 'MACS2.Prob.poisson_cdf' ignored Could you please help? Thanks!

taoliu commented 5 years ago

@YiqunCao See my reply at #265