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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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Q: atac-seq nolambda? #412

Open jfreimer opened 3 years ago

jfreimer commented 3 years ago

Hi,

I have seen most papers doing ATAC-Seq analysis run macs2 with the --nolambda option, including the hmmratac paper. Naively, it seems like this would overcall peaks/peak summits in generally open regions. Can you please explain why macs2 should be run with --nolambda for ATAC-Seq data?

Thanks

taoliu commented 3 years ago

@jfreimer --nolambda will let MACS2 only consider a genome-wide background, in another word, a single value (total_signal/genome_size), to calculate the p-value. Without setting it, MACS2 will estimate local background from ATAC-seq data. Since there is no 'control' data for ATAC-seq, the 'local background' from ATAC-seq itself will over-kill broad regions of chromatin accessibility.

ZHIDIHUAYUAN commented 3 years ago

Hi, could you please tell me more details about how macs2 estimate 'local background'? When I only focus on the peaks on chr6, could I only use the records of chr6 to call peaks and filt out other records of other chromosome？