preprocess

This module finds DEG in TSS and 5dist regions and preprocesses the data for dds_analysis.

Optional arguments:

  • -h, –help: Show the help message and exit.

Required arguments:

  • -in_folder IN_FOLDER, –in_folder IN_FOLDER: Input file folder for MRs overlapping with TSS and 5Distance regions that was done in dmr_analysis.

  • -in_string IN_STRING, –in_string IN_STRING: String that will appear in the output file of DMR regions overlapped with TSS or 5dist.

  • -in_tss_file_mr IN_TSS_FILE_MR, –in_tss_file_mr IN_TSS_FILE_MR: Path of a file that has DMR overlapped with TSS.

  • -in_dist_file IN_DIST_FILE, –in_dist_file IN_DIST_FILE: Path of a file that has DMR overlapped with 5dist.

  • -in_deg_file IN_DEG_FILE, –in_deg_file IN_DEG_FILE: Path of a file that has DEG and is exported using bpb3.

  • -out_folder OUT_FOLDER, –out_folder OUT_FOLDER: Output folder path.

  • -gene_col_name GENE_COL_NAME, –gene_col_name GENE_COL_NAME: Name of the gene column. See your DEG file and its header to find the column name.

  • -tss_file TSS_FILE, –tss_file TSS_FILE: Path of a file that has TSS regions.

  • -full_mr_file FULL_MR_FILE, –full_mr_file FULL_MR_FILE: File path of all ranked DMRs in the result folder of dmr_analysis.

  • -in_genome_file IN_GENOME_FILE, –in_genome_file IN_GENOME_FILE: Genome file path which contains refFlat file and enhancer files.