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adoebley / Griffin

A flexible framework for nucleosome profiling of cell-free DNA
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How to make site_lists #16

Closed RetGiraffe11235 closed 1 month ago

RetGiraffe11235 commented 11 months ago

Hi Developer,

Thank you for creating such a useful tool for tumor classification. I'm sorry for a lack of understanding of this tool, but how do we indicate the site file on the nucleosome_profiling step? I understood the current version of Griffin doesn't require site filtration prior to analysis. However, it still requires the site file. If I run Griffin using our data, can we divert the demo site file for running? Thank you for your great effort in maintaining this tool.

Best, Tomoki

liujilei156231 commented 11 months ago

+1

Looking forward to a response from the author team！

adoebley commented 1 month ago

Thanks for the question and sorry for the huge delay in responding! You can specify the sites file by modifying config/sites.yaml to include the name of your sites file and the path to that file. This is step 7 under "nucleosome profiling" in the Wiki:

  1. Open the sites.yaml (run_demo/griffin_nucleosome_profiling/config/sites.yaml) and update the path to the demo sites file:

    site_lists:
       CTCF_demo: ../../demo/griffin_nucleosome_profiling_demo_files/sites/CTCF.hg38.1000.txt

For instance if you have two sites files "sites1.txt" and "sites2.txt" you would modify the config to contain:

site_lists:
   sites1: path/to/sites1.txt    sites2: path/to/sites2.txt

Hope that helps! I'm going to close this issue for now but feel free to re-open it if you have follow up questions.