dmr_map2genome

Map DMR/MRs to predefined genomic regions such as TSS, TES, 5dist, etc.

Required Parameters

• in_cluster_out_path: File path that contains all clustered PWMs and uncertain PWMs. Example: ../data/out/sep8_run1.

• in_bpb3_ranking_path: File path for bpb3 ranking results. Example: ../data/out/sep8_run1/test_67snps/foreground/test_seq/rankings/.

• in_fileString4clustered_pwm: File string or file folder/name used/contained for clustered PWMs, such as quality_assessed_out_seed3.

Required

• -inSDFile IN_SORTEDDMR_FILE or --in_sortedDMR_file IN_SORTEDDMR_FILE: An exported file from DMR_analysis with BED format, such as the exported file from “dmr_combine_multChrs4rank,” where the columns are chrom, start_position, end_position, DMR_ID, and probability values. Please note that this input file should be sorted by chromosome position before being intersected with predefined genomic regions such as TSS, gene, or TES, etc.

• -inGRFile IN_GENEREGION_FILE or --in_geneRegion_file IN_GENEREGION_FILE: A list of gene region files that is generated by hmst_seq_analyzer, such as “list_region_files.txt,” where the file name and path of genomic region files are listed. These predefined genomic region files will be intersected with the sorted bed file of MR/DMR. Please refer to the demo of “run_hmsq.sh” for how to generate these predefined genomic region/annotation files.

• -inOFolder IN_OUTFILE_FOLDER or --in_outFile_folder IN_OUTFILE_FOLDER: Path of the output file folder for exporting intersected MR/DMR files with each genomic region.

• -inRefFile IN_REFFLAT_FILE or --in_refFlat_file IN_REFFLAT_FILE: Path of the input refFlat reference file, such as an export file “hg19.refFlat_clean_sorted.bed” from “hmst_seq_Analyzer”.

Optional Parameters

• -minOlp or --in_minimum_overlap4bedtools: Minimum overlap rate in bedtools intersection. The default is 1e-9 or 1 bp overlap, which is a float number between 0 and 1.