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:
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;
<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.