dmr_map2chromSegment

Map DMR/MRs to predicted chromatin segments from 6 human cell lines.

Required Parameters

  • -inFolder IN_CHROMATINSEGMENT_FILE_FOLDER or --in_chromatinSegment_file_folder IN_CHROMATINSEGMENT_FILE_FOLDER: Path of the input file folder containing combined chromatin segment files from six cells in BED format. The combined six cells *.bed.gz files can be downloaded from [https://genome.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeAwgSegmentation](https://genome.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeAwgSegmentation).

  • -outFolder IN_OUTFILE_FOLDER or --in_outFile_folder IN_OUTFILE_FOLDER: Path of the output file folder for DMR/MRs mapped to chromatin segments.

  • -inDFile IN_DMR_FILE or --in_DMR_file IN_DMR_FILE: Input DMR file name, which is a sorted export file from DMR_analysis with BED format, such as the export file from “dmr_combine_multChrs4rank”.

Optional Parameters

  • -inMinLen IN_MINIMUM_LENGTH4REGION or --in_minimum_length4region IN_MINIMUM_LENGTH4REGION: The minimum length for each selected chromatin segment. The default is 10 bp.

  • -inFileStr IN_FILENAME_STRING or --in_fileName_string IN_FILENAME_STRING: String name for input chromatin segment files that are stored in the folder. The default is *.bed.gz.

  • -OFileStr IN_OUTFILENAME_STRING or --in_outFileName_string IN_OUTFILENAME_STRING: Output file type string that will be used for output combined chromatin segment files. The default is “combined_six_cells_chromatin_segment_min”.

  • -inMinOp IN_MINIMUM_OVERLAP4BEDTOOLS or --in_minimum_overlap4bedtools IN_MINIMUM_OVERLAP4BEDTOOLS: The minimum overlap rate in bedtools intersection. The default is 1e-9 or 1 bp.

  • -inExist IN_COMBINED_CHROMATINSEGMENT_EXIST or --in_combined_chromatinSegment_exist IN_COMBINED_CHROMATINSEGMENT_EXIST: Indicates whether the combined six cell chromatin segment files exist or not. Use 0 for “not exist,” which means the -in_chromatinSegment_file_folder is the path for raw files downloaded. Use 1 if the combined six cell chromatin segment files are ready and sorted by chromosome position, where the path of -inFolder is the location of these combined files of six cells with filenames starting with “combined_six_cells_*.gz”. The default is 0.