homer2cmap - HOMER Hi-C matrix to ccmap or gcmap¶
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]
-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; <chromosome>_<resolution>_<suffix>.ccmap 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.