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biocore-ntnu / epic2

Ultraperformant reimplementation of SICER
https://doi.org/10.1093/bioinformatics/btz232
MIT License
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Start positions all end in 00 #33

Closed melemieux closed 5 years ago

melemieux commented 5 years ago

Hi,

I notice that all the peak Start positions end in "00" (including in your own examples). How is that possible?

Here's my command using epic2 v.0.0.41 under Ubuntu 18.04: epic2 --treatment input_rmdup.bam --control control_rmdup.bam --genome mm10 --mapq 10 --output test.bed

Thanks, Madeleine

melemieux commented 5 years ago

I've just re-read the description of the parameters so I see that the bin size is causing this behaviour. Can I set the bin size to 1 to increase the position resolution?

I guess I'll try!

endrebak commented 5 years ago

Thanks for creating an issue! No, epic2 is a great caller for diffusely spread out histone modifications, but the minimum recommended bin size is 50. If you require basepair resolution you should try something else like macs2 :)