Using curation with ms4alg.sort

[Bassir]

Based on the MS3 docs it seems the curate flag needs to be set to true to run automatic curation. Is there documentation on how to do this with ms4alg.sort?

[dragospekic]

Hello has this been answered elsewhere as I need to understand that as well. The sorting batch example doesn't seem to explain how to do automatic curation: https://github.com/flatironinstitute/mountainsort_examples/blob/master/bash_examples/001_ms4_bash_example/ms4_sort_bash.sh

[magland]

The docs will need to be updated. For now, please see the following for an example: https://github.com/edeno/franklab_sorting_pipeline

On Thu, Sep 26, 2019 at 11:35 AM dragospekic [email protected] wrote:

Hello has this been answered elsewhere as I need to understand that as well. The sorting batch example doesn't seem to explain how to do automatic curation:

https://github.com/flatironinstitute/mountainsort_examples/blob/master/bash_examples/001_ms4_bash_example/ms4_sort_bash.sh

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[ralbso]

I can't find any reference to the curation with ms4alg itself in that link. It's all python code, and the call to ml_ms4alg doesn't include a curation parameter. Am I missing something here?

[magland]

See the code in here: https://github.com/edeno/franklab_sorting_pipeline/blob/master/sort_animal_day.py

It computes metrics used for curation, makes a label map, and applies a label map.