Effective Genome Size

[c-guzman]

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Is this just because the parameter information is outdated or will this result in incorrect peak calling?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]

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.

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On Saturday, April 15, 2017, Carlos Guzman ***@***.***> 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 Is this just because the parameter information is outdated or will this result in incorrect peak calling?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! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#51>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AQ9I0gJjWmZAjuojPZG8rgfhywztsbBQks5rwEFCgaJpZM4M-PjN> .

[c-guzman]

Great, thank you!