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CCRGeneticsBranch / Oncogenomics_v2

Oncogenomics portal version 2
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Add cnvkit gene level #47

Open hsienchao opened 6 months ago

hsienchao commented 6 months ago

Previously we intersected the cnvkit segment file with gene coordinates but the results might not be accurate if the gene is very short. Instead we should use command cnvkit.py genemetrics command to generate gene level log2 ratio from bin files.

To process the existing files on Frederick servers, I've Jiqui to install cnvkit for us. Now I processed one case (CHP212) and updated the web interface. I plan to run all samples next week.

hsienchao commented 5 months ago

I have rerun 3500+ current cnvkit samples. Now I am uploading them to DB.

hsienchao commented 5 months ago

Finished. I also generated the table of COG_UK and sent it to Xinyu.