The example hic file cannot be dumped about chess HOT 4 CLOSED

Hi all,

I found that the fanc could be used to convert the valid pairs generated by HiC-Pro to hic format, and also do normalization and visualization. So, I have changed to use fanc to generate the input for chess. Here, I am closing the issue, but feel free to reopen it.

Best wishes,
Zheng zhuqing

from chess.

Hi @biozzq ,
the example files are in FAN-C format, not Juicer. You can either visualize them with the FAN-C API (here is the repo with a link to the docs) or convert the files to Juicer format with fanc to-juicer.

from chess.

Dear @nickmachnik

Sorry, I found the command you provided can convert a readpairs file to Juicer .hic format. Meanwhile, I cannot find any more usage instructions about the fanc to-juicer in the following link https://vaquerizaslab.github.io/fanc/getting_started.html. Please let me know if I missed anything.

fanc to-juicer -h
2020-11-21 22:44:44,526 INFO FAN-C version: 0.9.7
usage: fanc hic_to_juicer [-h] [--juicer-tools-jar JUICER_TOOLS_JAR_PATH] [-tmp] [-r RESOLUTIONS [RESOLUTIONS ...]] input [input ...] output

Convert a ReadPairs file to Juicer .hic format

positional arguments:
input Input .pairs file(s), FAN-C format.
output Output Juicer file.

optional arguments:
-h, --help show this help message and exit
--juicer-tools-jar JUICER_TOOLS_JAR_PATH
Path to juicer jar. You can also specify this in fanc.conf
-tmp, --work-in-tmp Work in temporary directory
-r RESOLUTIONS [RESOLUTIONS ...], --resolutions RESOLUTIONS [RESOLUTIONS ...]
Resolutions in bp at which to "zoom" the juicer matrix.

Best wishes,
Zhuqing

from chess.

Hi @biozzq ,
sorry, you are right, you actually won't be able to convert the example files to juicer with that command, my bad.
There is a fanc to-cooler command that you could use to convert to cooler format, but I have no idea whether that is helpful at all. Maybe you could alternatively use fanc's command line tools for plotting or its python api.

from chess.