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XiaoTaoWang / HiCLift

A fast and efficient tool for converting chromatin interaction data between genome assemblies
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Output as .cool format instead of .mcool #9

Open mb6434 opened 1 year ago

mb6434 commented 1 year ago

Hi,

Thank you very much for the development of this tool. I am facing an issue regarding the output format.

Here is the cmd line which I used:

HiCLift --input $file.cool --input-format cooler --out-pre test --output-format cool --out-chromsizes mm10_2.sizes --in-assembly mm9 --out-assembly mm10

I would like to know how could you got a .cool format instead of .mcool.

And also, I am not familiar with the argument --high-res, would you please develop a little bit?!

Thank you for your help and time,

Best regards,

Mathilde

XiaoTaoWang commented 1 year ago

Hi Mathilde,

.mcool is just an extension of .cool which stores contact matrices at multiple resolutions, and it's quite straightforward to extract the contact matrices at a specific resolution into a .cool file. Suppose your output .mcool file name is "test.mm10.mcool", and you want to extract the contact matrix at 5kb, just execute the cooler cp command below::

$ cooler cp test.mm10.mcool::resolutions/5000 test.mm10.5kb.cool

You can use the cooler ls command to list all individual cool files (cool URIs) within a .mcool file::

$ cooler ls test.mm10.mcool

By default, the highest resolution of contact matrices reported by HiCLift is 5kb. By specifying "--high-res", the highest reported resolution will be set to 1kb.

Best, Xiaotao

mb6434 commented 1 year ago

Hi Xiaotao,

Thank you very much for your answer and to give to me solutions. This is awesome!

Best reagrds,

Mathilde