WIP cleanup hit calling notebook

broadinstitute / 2022_PERISCOPE

This repository contains all supporting analyses and files for Ramezani, Bauman, Singh, and Weisbart, et al. "A genome-wide atlas of human cell morphology".

BSD 3-Clause "New" or "Revised" License

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WIP cleanup hit calling notebook #2

Closed ErinWeisbart closed 1 year ago

ErinWeisbart commented 1 year ago

@MerajRamezani I'm using this branch to clean up the "Hit_Calling" and "Profile_Aggregation" folders.

A few questions I need you to address about Hit_Calling:

[x] I was able to find in your code in the data analysis repo the CCLE_expression data for HeLa. I need the CCLE_expression .csv you used for A549.
[x] What version of the DepMap data did you used to generate these files (e.g. DepMap Public 22Q2)
[x] Exactly how did you get from the raw file you downloaded from DepMap to the CCLE_expression .csv's you used for Hit Calling?
[ ] what is zero_tpm and how is it different than unexpressed?

ErinWeisbart commented 1 year ago

Questions about Profile_Aggregation:

[x] Your DMEM notebook has heat_map and clustered_heat_map as outputs but your A549 and HPLM notebooks do not. Are these maps used somewhere in a figure? i.e. should they be generated for all three screens or removed?

From conversation with Meraj: those outputs are not used and can be deleted. They were sanity checks.

ErinWeisbart commented 1 year ago

I went ahead and created a new CCLE_expression.csv that incorporates both HeLa and A549 data and detailed how in the README.md in https://github.com/broadinstitute/2022_PERISCOPE/pull/2/commits/667b47125de4de3a0505b2f0ed50b6f7d05b7255. So that addresses most of what I asked of you above, Meraj. One question is still outstanding.