hicConvertFormat

usage: hicConvertFormat --matrices MATRICES [MATRICES ...] --outFileName

                        OUTFILENAME [OUTFILENAME ...] --inputFormat

                        {h5,cool,hic,homer,hicpro} --outputFormat

                        {cool,h5,homer,ginteractions,mcool}

                        [--correction_name CORRECTION_NAME]

                        [--correction_division] [--store_applied_correction]

                        [--chromosome CHROMOSOME] [--enforce_integer]

                        [--load_raw_values]

                        [--resolutions RESOLUTIONS [RESOLUTIONS ...]] [--help]

                        [--version]

                        [--bedFileHicpro BEDFILEHICPRO [BEDFILEHICPRO ...]]

---

Conversion of Hi-C matrices of different file formats to cool.

Required arguments:

  --matrices MATRICES [MATRICES ...], -m MATRICES [MATRICES ...]

                        input file(s). Could be one or many files. (default:

                        None)

  --outFileName OUTFILENAME [OUTFILENAME ...], -o OUTFILENAME [OUTFILENAME ...]

                        File name to save the exported matrix. (default: None)

  --inputFormat {h5,cool,hic,homer,hicpro}

                        file format of the matrix file. The following options

                        are available: `h5` (native HiCExplorer format based

                        on hdf5 storage format), `cool`, `hic`, `homer`,

                        `hicpro` (default: None)

  --outputFormat {cool,h5,homer,ginteractions,mcool}

                        Output format. The following options are available:

                        `h5` (native HiCExplorer format based on hdf5 storage

                        format). `cool` and `ginteractions` (default: cool)

Optional arguments:

  --correction_name CORRECTION_NAME

                        Name of the column which stores the correction

                        factors. The information about the column names can be

                        figured out with the tool hicInfo. Option only for

                        cool input files. (default: weight)

  --correction_division

                        If set, division is applied for correction. Default is

                        a multiplication. Option only for cool input files.

                        (default: False)

  --store_applied_correction

                        Store the applied correction and do not set correction

                        factors. Option only for cool input files. (default:

                        False)

  --chromosome CHROMOSOME

                        Load only one chromosome. Option only for cool input

                        files. (default: None)

  --enforce_integer    Enforce datatype of counts to integer. Option only for

                        cool input files. (default: False)

  --load_raw_values    Load only 'count' data and do not apply a correction.

                        Option only for cool input files. (default: False)

  --resolutions RESOLUTIONS [RESOLUTIONS ...], -r RESOLUTIONS [RESOLUTIONS ...]

                        List of resolutions that should be added. (default:

                        None)

  --bedFileHicpro BEDFILEHICPRO [BEDFILEHICPRO ...], -bf BEDFILEHICPRO [BEDFILEHICPRO ...]

                        Bed file(s) of hicpro file format. (default: None)

这个应该是：hicpro-> hicexplorer所需要的bed。

转出来的只有ginteractions可以看见格式：如下500kb：

转下hicpro的输出看看：

hicConvertFormat --matrices dixon_2M_50000.matrix --inputFormat hicpro --outFileName dixon_2M_50000.h5 --outputFormat h5 --bedFileHicpro dixon_2M_50000_abs.bed