MACS2 ATAC-Seq Help! Danio Rerio?

Question

[kyle.s.shank]

Hello all,

I'm currently fleshing out the middle part of an ATAC-seq pipeline for a Zebrafish study, and I'm running into a bit of a wall with my MACS2 parameters. I want to pass a value to -g (effective genome size), but I'm running into a problem finding any valid effective genome sizes for Dario Rerio. Does anyone out there have a better value than me just taking 70% of the total genome length?

Thanks for all the help,

• Kyle Shank

Answer 1

[Sinji]

EPIC has a script meant to calculate the effective genome size. This may work for you.

[kyle.s.shank]

Thanks! I appreciate the help.