Output File Naming

• Filtered Files: Files are always given a .filtered extension before the file format when passed into the output directory (e.g., file.filtered.bed.gz).

• Command-Processed Files: Files processed by a Finaletoolkit command have the command name (with underscores) inserted before their format (e.g., file.frag_length_bins.bed.gz).

• Multiple Commands: Input files will be processed for each enabled Finaletoolkit command.