check_block_gene_inTAD

Check whether mutation blocks and genes are in the same TAD or TAD boundary.

Optional Arguments:

• -h, –help: Show this help message and exit

Required Arguments:

• -in_BGfile IN_FILTERED_BLOCKUQGENE_FILE, –in_filtered_blockUqGene_file IN_FILTERED_BLOCKUQGENE_FILE: Input filtered block and gene information file with unique gene name that is exported by dds_analysis collect_gene_names4blocks

• -in_GPfile IN_GENE_POSITION_FILE, –in_gene_position_file IN_GENE_POSITION_FILE: Input gene position file, a bed format file that indicates all gene start positions and end positions, which can be generated by hmst-seq-analyzer using a refFlat file

• -in_TPfile IN_TAD_POSITION_FILE, –in_TAD_position_file IN_TAD_POSITION_FILE: Input Topologically Associating Domain (TAD) position file, a bed format file that describes each TAD’s start and end positions, sorted by chromosome position

• -in_TBfile IN_TAD_BOUNDARY_FILE, –in_TAD_boundary_file IN_TAD_BOUNDARY_FILE: Input Topologically Associating Domain (TAD) boundary file, a bed format file that indicates each TAD boundary’s start and end positions, sorted by chromosome position