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tanlongzhi / dip-c

Tools to analyze Dip-C (or other 3C/Hi-C) data
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Can not colored #60

Closed XiongGZ closed 11 months ago

XiongGZ commented 11 months ago

Hi Tan, @tanlongzhi

When i try to colored the chromosomes and cpg island, the command run successfully, but can not write the colors. Can you help me to solve this problem?

Commond: dip-c color -c $dip_c/color/mm10.cpg.20k.txt patski.G2M.3dg

patski.G2M.3dg: image

mm10.cpg.20k.txt: image

Results: image

tanlongzhi commented 11 months ago

Looks like your genome reference file for mapping (and hence your .3dg file) has chromosomes named like "Y", while my color files have the mouse chromosomes named like "chrY", causing a mismatch.

XiongGZ commented 11 months ago

Looks like your genome reference file for mapping (and hence your .3dg file) has chromosomes named like "Y", while my color files have the mouse chromosomes named like "chrY", causing a mismatch.

I deleted the chromosome Y and X, but it still don't work grep -v -E "^Y|^X" patski.G2M.3dg > test.3dg

test.3dg: image

Command: dip-c color -c $dip_c/color/mm10.cpg.20k.txt test.3dg

Result: image

tanlongzhi commented 11 months ago

There will still be mismatch like "13" vs "chr13". You must rename all your chromosomes.

XiongGZ commented 11 months ago

There will still be mismatch like "13" vs "chr13". You must rename all your chromosomes.

It worked. Thanks!