MergeTotal

Here we discuss the use of the MergeTotal command, which follows the `MergeCelltype' command and merges a defined set of cell types into one cohort fragment file. This final file is the necessary input for training the ChromBPNet Tn5 bias model in the Model Training section.

Usage

MergeTotal \
    '$sample_directory' \
    '$output_directory'

Input Format

Required arguments:
sample_directory   # Directory containing the merged (pseudo-bulked) cell type fragment files (e.g., ~/atac_seq_data/mouse_merged)
output_directory   # Directory for the output merged fragment file. Often the same path, for ease of use. 

Output Format

The following fragment file name and associated indexed file will be the sole output of this function.

~/atac_seq_data/mouse_merged/all_cells_merged_sorted.tsv.gz