Contains code to replicate genetic mapping and figures for pQTN manuscript:
https://www.biorxiv.org/content/10.1101/2024.10.18.619054v1
Functions and example Snakemake file for pQTN mapping on SWATH-MS data.
plotting_master_script.m will generate the figures in the manuscript. Specify your local code_directory, desired output_directory for the figure files, and download the dependencies (below) and specify the dependency_directory to run the script.
The mapping and plotting code depends on various input data that can be found here (~ 9 Gb on disk): https://www.dropbox.com/scl/fo/3xbcbe9ivwz8aahrlk137/APGxHor01S7jnNX3a1Yk3Og?rlkey=yx81ckrtaq8eb5pu80ggprjhs&dl=0
Upon acceptance, a snapshot of the dependencies and code to reproduce the final figures will be available on Zenodo.