pinellolab / ampumi Goto Github PK

I would like to use AmpUMI code in a UMI pipeline, but I do not see an open source license listed. Might I suggest either adding an open source license, or stating in the README that the code is not licensed for open source use? Thank you. https://docs.github.com/en/communities/setting-up-your-project-for-healthy-contributions/adding-a-license-to-a-repository https://choosealicense.com/

Very useful tool, thank you. I was wondering, whether, respectively how the calculations for collision probabilty and collision numbers can be adapted to allow arbitrary edit distances when doing the UMI clustering. This would make AmpUMI useful also for assessing UMI applications with more error-prone third-gen sequencing data (like in PMID: 33432244).

Thank you
Best, Stefan

Hello, could you help me please? After installing the program and specifying the path, the program does not start. When I write AmpUMI h- and other, it says that there is no such command. What is the problem?

I would like to know how to calculate the number of molecules in a experiment. In targeted DNA seq, it has something to do with coverage? Million reads per sample? Amplicons per run?
Thanks

pip install git+git://github.com/pinellolab/AmpUMI.git
should be
pip install git+https://github.com/pinellolab/AmpUMI.git