Open jeff-godwin opened 4 months ago
Hello,
I have a question regarding the filtering of low count bins.
The nextflow (v2.1.0) results produces balanced cooler files. Am I correct to assume this is from the "cooler balance" functionality? And is the --mad-max parameter running on the default value of 5 (https://cooler.readthedocs.io/en/latest/cli.html#cooler-balance) ? In HiCexplorer, one can calculate the mad-max filter using (https://hicexplorer.readthedocs.io/en/latest/content/tools/hicCorrectMatrix.html). Over here, https://github.com/open2c/cooler/issues/140, it is mentioned that both filtering are equivalent. I want to clarify if the balance cool file needs any further filtering?
Many thanks, Jeffrey
Hello,
I have a question regarding the filtering of low count bins.
The nextflow (v2.1.0) results produces balanced cooler files. Am I correct to assume this is from the "cooler balance" functionality? And is the --mad-max parameter running on the default value of 5 (https://cooler.readthedocs.io/en/latest/cli.html#cooler-balance) ? In HiCexplorer, one can calculate the mad-max filter using (https://hicexplorer.readthedocs.io/en/latest/content/tools/hicCorrectMatrix.html). Over here, https://github.com/open2c/cooler/issues/140, it is mentioned that both filtering are equivalent. I want to clarify if the balance cool file needs any further filtering?
Many thanks, Jeffrey