Do I have to use PEPPRO with looper?
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?
To run using
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.
|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%|