Do I have to use PEPPRO with looper?

No. PEPPRO by itself does not specify any cluster resources, so you could just roll your own and submit individual jobs to a cluster however you choose. But because PEPPRO is already looper-compatible, the easier way is to use looper's built-in template system, which looper uses to build flexible shell scripts for job submission. These templates can be used to run jobs in a container, to submit to a cluster resource manager, or both.

Will PEPPRO run on a mac?

The pipeline has been successfully run in both a Linux and MacOS environment.

Can I run the project used in the paper?

Of course! Here is the exact project configuration file and project annotation file.

To run using looper:

looper run peppro_paper.yaml

How do I determine if my samples are good quality?

To assist in determining whether you are working with a good quality nascent RNA library, we recommend several cutoffs for PEPPRO quality metrics that can be used to help make this decision. If your sample meets or exceeds these values, it suggests it is a high quality sample.

Metric Recommended value
Degradation ratio < 1
rDNA alignment rate < 20%
Pause index > 10
mRNA contamination 1 - 1.5
% uninformative adapter reads < 25%
TSS enrichment (coding) > 10
TSS enrichment (non-coding) > 5
% unique at 10M reads > 75%