summary.md

Summary

Analysis run by Snakefile using this config file. See the README in the top directory for details.

Here is the rule graph of the computational workflow:

Here is the Markdown output of each notebook in the workflow:

1. Get prior RBD DMS mutation-level binding and expression measurements and barcode-variant lookup table from the SARS-CoV-2-RBD_DMS_Omicron repository and the original DMS library for SARS-CoV-2 (PCR-based mutagenesis) here.

2. Count variants and then aggregate counts for Wuhan_Hu_1, Omicron_BA1, and Omicron_BA2 to create variant counts files for Wuhan_Hu_1, Omicron_BA1, and Omicron_BA2.

3. Analyze sequencing counts to cells ratio for Wuhan_Hu_1, Omicron_BA1, and Omicron_BA2 this prints a list of any samples where this ratio too low. Also creates a CSV for Wuhan_Hu_1, Omicron_BA1, and Omicron_BA2 with the sequencing counts, number of sorted cells, and ratios for all samples.

4. Calculate escape scores from variant counts for Wuhan_Hu_1, Omicron_BA1, and Omicron_BA2.

5. Call sites of strong escape for Wuhan_Hu_1, Omicron_BA1, and Omicron_BA2.

6. Plot escape profiles for Wuhan_Hu_1, Omicron_BA1, and Omicron_BA2.

7. Map escape profiles to *.pdb files using notebooks here for Wuhan_Hu_1, Omicron_BA1, and Omicron_BA2.

8. Make supplementary data files for Wuhan_Hu_1, Omicron_BA1, and Omicron_BA2, which are here for Wuhan_Hu_1, Omicron_BA1, and Omicron_BA2. These include dms-view input files.