bc2cmap -Bin-Contact files pair to ccmap or gcmap¶
In this format, two separate files are available. One file contains bins information and other contains contact frequency.
- These types of files are present in following GEO data:
- This format contains a pair of file:
- BIN file:
cbin chr from.coord to.coord count 1 2L 0 160000 747 2 2L 160000 320000 893 3 2L 320000 480000 1056 4 2L 480000 640000 1060 5 2L 640000 800000 978 6 2L 800000 960000 926 . . .
- CONTACT file in list format:
cbin1 cbin2 expected_count observed_count 1 1 40.245201 21339 1 2 83.747499 5661 1 3 92.12501 1546 1 4 93.401273 864 1 5 87.265472 442 . . .
Both BIN and CONTACT files are necessary for the conversion.
usage: gcMapExplorer bc2cmap [-h] [-ib nm_none_160000.bins] [-ic nm_none_160000.n_contact] [-ccm RawObserved] [-od OUTDIR] [-gcm inOut.gcmap] [-cmeth lzf] [-dmeth sum] [-wd /home/rajendra/deskForWork/scratch]
-h, --help show this hel p message and exit -ib nm_none_160000.bins, --input-bin nm_none_160000.bins Input BIN file as shown above. -ic nm_none_160000.n_contact, --input-contact nm_none_160000.n_contact Input CONTACT file as shown above. -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.