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XiaoTaoWang / HiCLift

A fast and efficient tool for converting chromatin interaction data between genome assemblies
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How to draw a beautiful HIC map #14

Open songxh1996 opened 10 months ago

songxh1996 commented 10 months ago

Hello, Professor Wang, thank you for providing so much useful software. I tried a lot of software, such as fanc,hicexplorer, but did not draw the hic map I wanted. I was so lucky to see this beautiful HIC map in you. But I didn't find out how you drew it, whether I missed what it was. How do you draw a beautiful HIC map? Which script is used

fig1 svg p4jkei4a

XiaoTaoWang commented 10 months ago

Hi, you may refer to this page as a reference https://xiaotaowang.github.io/TADLib/visualize.html

songxh1996 commented 10 months ago

Thank you very much for your help. When I finished running the test data according to your guidance, it was successful. But when I used my own data, it failed. I can't figure out why.

my cool file ##########.hic2.cool hicConvertFormat -m LD_nomt.allValidPairs.hic --inputFormat hic --outputFormat cool -o KR_matrix.cool -r 10000 --correction_name KR ###########hic-pro result covert cool cooler load -f coo LD_nomt_10000_abs.bed LD_nomt_10000_iced.matrix 10000.cool --count-as-float

vis = Triangle('GM12878-MboI.hg19.cool::10000', '21', 45000000, 46500000) vis = Triangle('10000.cool::10000', 'NC_059157.1', 4500000, 4650000) Traceback (most recent call last): File "", line 1, in File "/home/songxianhan/miniconda3/envs/test/lib/python3.7/site-packages/tadlib/visualize/heatmaps.py", line 18, in init self.clr = cooler.Cooler(uri) File "/home/songxianhan/miniconda3/envs/test/lib/python3.7/site-packages/cooler/api.py", line 85, in init self._refresh() File "/home/songxianhan/miniconda3/envs/test/lib/python3.7/site-packages/cooler/api.py", line 106, in _refresh raise KeyError(err_msg) from None KeyError: "No cooler found at: 10000.cool. Coolers found in ['/']. Use '::' to specify a group path"

XiaoTaoWang commented 10 months ago

Can you try the following command instead:

vis = Triangle('10000.cool', 'NC_059157.1', 4500000, 4650000)
songxh1996 commented 10 months ago

When I use this code, the error persists.

vis = Triangle('40000.cool', 'NC_059157.1', 4500000, 4650000) Traceback (most recent call last): File "", line 1, in File "/home/songxianhan/miniconda3/envs/tset/lib/python3.7/site-packages/tadlib/visualize/heatmaps.py", line 18, in init self.clr = cooler.Cooler(uri) File "/home/songxianhan/miniconda3/envs/tset/lib/python3.7/site-packages/cooler/api.py", line 85, in init self._refresh() File "/home/songxianhan/miniconda3/envs/tset/lib/python3.7/site-packages/cooler/api.py", line 106, in _refresh raise KeyError(err_msg) from None KeyError: "No cooler found at: 40000.cool. Coolers found in ['/40000']. Use '::' to specify a group path"

XiaoTaoWang commented 10 months ago

Can you show the result after you execute the following command?

$ cooler ls 40000.cool