homer2cmap - HOMER Hi-C matrix to ccmap or gcmapΒΆ

HOMER package contains modules to analyze genome wide interaction data. It creates Hi-C matrix in a specific format as shown as shown here.

This format contains contact map in a matrix format.

usage: gcMapExplorer homer2cmap [-h] [-i matrix.txt] [-ccm RawObserved]
                                [-od OUTDIR] [-gcm inOut.gcmap] [-cmeth lzf]
                                [-dmeth sum]
                                [-wd /home/rajendra/deskForWork/scratch]

Optional arguments:

-h, --help            show this help message and exit
-i matrix.txt, --input matrix.txt
                       File containing HOMER Hi-C ineraction matrix format contact map

-ccm RawObserved, --ccmap RawObserved
                       Use this to convert all contact maps to ccmaps file. Provide suffix of
                      ccmap file names with this option and it will enable the conversion.

                      Output ccmap file name is generated automatically as follows;

                      Note that -od/--out-dir option is also required because all ccmaps will be
                      saved in this directory.

-od OUTDIR, --out-dir OUTDIR
                      Directory where all ccmap files will be saved.
-gcm inOut.gcmap, --gcmap inOut.gcmap
                      Provide gcmap file to convert all contact maps into one gcmap file.
                      File name should contain full path because -od/--out-dir is not considered
                      for thi conversion.

-cmeth lzf, --compression-method lzf
                      Data compression method for gcmap file.
-dmeth sum, --downsample-method sum
                      Downsampling method to coarsen the resolution in gcmap file. The option is
                      intended to use with -gcm/--gcmap option. Three accepted methods are
                              sum  : sum of values,
                              mean : Average of values and
                              max  : Maximum of values.

                      This option generates all coarser maps where resolutions will be coarsened by
                      a factor of two, consecutively. e.g.: In case of 10 kb input resolution,
                      downsampled maps of "20kb", "40kb", "80kb", "160kb", "320kb" etc. will be
                      generated until, map size is less than 500.

-wd /home/rajendra/deskForWork/scratch, --work-dir /home/rajendra/deskForWork/scratch
                      Directory where temporary files will be stored.