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hicluster filter-contact

hicluster filter-contact#

This step shows the first step for processing the HiC contact files, involving remove blacklist regions and filter the minimum length of contacts.

Command Docs#

usage: hicluster filter-contact [-h] --contact_table CONTACT_TABLE
                                --chrom_size_path CHROM_SIZE_PATH
                                [--output_dir OUTPUT_DIR]
                                [--blacklist_1d_path BLACKLIST_1D_PATH]
                                [--blacklist_2d_path BLACKLIST_2D_PATH]
                                [--blacklist_resolution RESOLUTION_2D]
                                [--not_remove_duplicates] [--chr1 CHROM1]
                                [--pos1 POS1] [--chr2 CHROM2] [--pos2 POS2]
                                [--min_pos_dist MIN_POS_DIST] [--cpu CPU]

optional arguments:
  -h, --help            show this help message and exit
  --output_dir OUTPUT_DIR
                        Path to the output directory of the contact filesafter
                        blacklist filtering (default: None)
  --blacklist_1d_path BLACKLIST_1D_PATH
                        Path to blacklist region BED file, such as ENCODE
                        blacklist. Either side of the contact overlapping with
                        a blacklist region will be removed. (default: None)
  --blacklist_2d_path BLACKLIST_2D_PATH
                        Path to blacklist region pair BEDPE file. Both side of
                        the contact overlapping with the same blacklist region
                        pair will be removed. (default: None)
  --blacklist_resolution RESOLUTION_2D
                        Resolution in bps when consider the 2D blacklist
                        region pairs. (default: 10000)
  --not_remove_duplicates
                        If set, will NOT remove duplicated contacts based on
                        [chr1, pos1, chr2, pos2] values (default: True)
  --chr1 CHROM1         0 based index of chr1 column. (default: 1)
  --pos1 POS1           0 based index of pos1 column. (default: 2)
  --chr2 CHROM2         0 based index of chr2 column. (default: 5)
  --pos2 POS2           0 based index of pos2 column. (default: 6)
  --min_pos_dist MIN_POS_DIST
                        Minimum distance for a contact to be kept. (default:
                        0)
  --cpu CPU             Number of cpus to parallel. (default: 20)

required arguments:
  --contact_table CONTACT_TABLE
                        Contain all the cell contact file information in two
                        tab-separated columns: 1. cell_uid, 2. file_path. No
                        header (default: None)
  --chrom_size_path CHROM_SIZE_PATH
                        Path to UCSC chrom size fileContain all the chromosome
                        information in two tab-separated columns: 1.
                        chromosome name, 2. chromosome length. No header
                        (default: None)

Command Example#

Here is an example of processing snm3C-seq data of mouse brain.

hicluster filter-contact \
    --output_dir rmbkl \
    --blacklist_1d_path /data/aging/ref/m3C/mm10-blacklist.v2.bed.gz \
    --blacklist_2d_path /data/aging/ref/m3C/mm10_2d_blacklist.bedpe.gz \
    --cpu 20 \
    --chr1 1 \
    --pos1 2 \
    --chr2 5 \
    --pos2 6 \
    --contact_table contact_table.tsv \
    --chrom_size_path /data/aging/ref/m3C/mm10.main.nochrM.nochrY.chrom.sizes

Command Breakdown#

--contact_table contact_table.tsv

Specify the file paths of the contact files in this line(e.g. /data/AMB-F-mapping/pool_amb64/mapping_000024/mapping_000024/hic/AMB_220712_18mo_12D_13B_2_P4-1-I15-A13.hisat3n_dna.all_reads.3C.contact.tsv.gz). Here is an example of what the contact table looks like:

cell_1  absolute_hic_contact_path_1
cell_2  absolute_hic_contact_path_2
cell_3  absolute_hic_contact_path_3

The first column indicates the cell name (e.g. AMB_220712_18mo_12D_13B_2_P4-1-I15-A13) whereas the second column indicates the hic contact file path of the cell. Make sure the two parts are separated by a tab; also make sure the file has no header.

--output_dir rmbkl

Will be automatically created if not existing already.

--blacklist_1d_path /data/aging/ref/m3C/mm10-blacklist.v2.bed.gz
--blacklist_2d_path /data/aging/ref/m3C/mm10_2d_blacklist.bedpe.gz

Both 1d and 2d blacklist could be downloaded from zhoujt1994/scHiCluster. We usually use the encode blacklist as the 1d blacklist, and 2d blacklist could be specific to the technologies and mapping strategies. We used the snm3C-seq mapping pipeline to map the snmC-seq data and obtained the potential false positive contacts as the 2d blacklist.

--chr1 1
--pos1 2
--chr2 5
--pos2 6

Specify which columns correspond to the positions of the two anchors of contacts. Note that the number is zero based, so the example above means 2nd and 3rd columns are the left anchor, and 6th and 7th columns are the right anchor. This format is the same juicer short format, and the standard output format of yap mapping pipeline.

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