<h1> Suggested_Solution Directory </h1> This section explains each of the files and folders in the Suggested_Solution directory in detail. Many of the files are similar to the files found in [Output - All Solutions](https://osf.io/t6j7u/wiki/5.%20Output%20-%20All%20Solutions/) and it is recommended to refer to that section for similar files. The files that are original to this directory will be indicated. @[toc](Sections) ---------- ## Output Overview ## Here is an overview of the file structure for Suggested_Solution:  In the following sections, the files that differ from those found All_Solutions will be examined. ## COSMIC_SBS96_Decomposed_Solution ## There are two files in `COSMIC_SBS96_Decomposed_Solution` that are not found in All_Signatures. 1. De_Novo_map_to_COSMIC_SBS96.csv 2. SBS96_Decomposition_Plots.pdf ### De_Novo_map_to_COSMIC_SBS96.csv ### This file contains data on the de novo extracted signatures and the COSMIC signatures that compose them. Additionally information on the L1 error %, L2 error %, [KL divergence](https://en.wikipedia.org/wiki/Kullback%E2%80%93Leibler_divergence), cosine similarity, and correlation. Below is an example of what the file contains.  ### SBS96_Decomposition_Plots.pdf ### This file contains a visualization of the results from `De_Novo_map_to_COSMIC_SBS96.csv`. There are two plots to the left of the curly brace. One is the original de novo signature plot and the other is the reconstruction of the de novo signature. On the right side of the curly brace are the COSMIC signatures that the de novo signature is composed of. Additionally, below the reconstructed plot are the data for cosine similarity, correlation, L1 error %, L2 error %, and KL divergence.  ## De_Novo_Solution ## There are two files in the `De_Novo_Solution` directory not found in All_Signatures. 1. De_Novo_Mutation_Probabilities_refit.txt 2. SBS96_De-Novo_refit_Signature_Assignment_log.txt ### De_Novo_Mutation_Probabilities_refit.txt ### This file contains the mutation probability for each sample and identified signature. Each of the signature mutation probabilities for a sample add up to 1. Below is an example of the first few lines of the example file.  ### SBS96_De-Novo_refit_Signature_Assignment_log.txt ### This file logs the events that occur when COSMIC signatures are assigned to samples. Below is an example of the start of the log file.