Error while running entropy as in help

[assafgrw]

I run the following: modkit entropy --in-bam ${mod_bam}
-o ${output_entropy_bedgraph}
--ref ${ref}
--threads 32
--log-filepath modkit_entropy.log

and get the following error:

Error! invalid input options, must provide --motif, --base, or specify --cpg

Any ideas?

[ArtRand]

Hello @assafgrw,

I apologize, this example in the documentation is out of date. I'll update it with the next version release.

You need to specify how to calculate the methylation entropy with --cpg, --base {A, C, G, T} or --motif. If you're in a mammalian system like human, I recommend using --cpg.