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biocore-ntnu / epic

(DEPRECATED) epic: diffuse domain ChIP-Seq caller based on SICER
http://bioepic.readthedocs.io
MIT License
31 stars 6 forks source link

Effective Genome Size #51

Closed c-guzman closed 6 years ago

c-guzman commented 7 years ago

As part of a pipeline I am using your epic-effective script to calculate EGS prior to downstream analysis. I was going through your arguments and noticed that your -egs parameter requires a EGS between 0 and 1. As opposed to the typical ~2.8 billion that is used by macs2 and deeptools for human hg38. I tried running epic with the 2.8 billion number and didn't run into any errors.

Is this just because the parameter information is outdated or will this result in incorrect peak calling? I'm interested in knowing if i'll have to parse out extra information or if what I already have done is fine.

Thanks!

endrebak commented 7 years ago

Egs: effective size divided by actual size. It is the same as the original SICER uses.

I should add an error if the EGS is bigger than one.

On Saturday, April 15, 2017, Carlos Guzman notifications@github.com wrote:

As part of a pipeline I am using your epic-effective script to calculate EGS prior to downstream analysis. I was going through your arguments and noticed that your -egs parameter requires a EGS between 0 and 1. As opposed to the typical ~2.8 billion that is used by macs2 and deeptools. I tried running epic with the 2.8 billion and didn't run into any errors.

Is this just because the parameter information is outdated or will this result in incorrect peak calling? I'm interested in knowing if i'll have to parse out extra information or if what I already have done is fine.

Thanks!

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c-guzman commented 7 years ago

Great, thank you!