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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

Usage with multiple treatments and controls #35

Closed ksiklenka closed 8 years ago

ksiklenka commented 8 years ago

If I have ChIP experiments on multiple different treatment groups (lets say dosage A B C D and a control group) how should I input into epic? Do I list the different treatment in a single command and epic treats them separately? Or should I run epic for each treatment vs a control.

Also that brings me to confusion in wordage for the control flag. Is it reads from an actual ChIP input (i.e no antibody chromatin DNA) or the IP of an untreated control group?

endrebak commented 8 years ago

1)

I would run the all files related to each dosage group separately.

so epic -t A1.bed A2.bed -c A_I1.bed A_I2.bed, then epic -t B1.bed B2.bed -c B_I1.bed B_I2.bed

2)

The first, I was not thinking of control groups when writing that. If you could suggest a wording that sounds better to biologists, please help me :)

endrebak commented 8 years ago

By the way, epic contains an option to print a gzipped-matrix of bin counts from your experiment. These can be used to run linear models on your results afterwards. See --store-matrix.

Closing this, but feel free to ask more related questions here or start a new thread.