Error while trying to convert 3dg file

lh3 / hickit

TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C

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Error while trying to convert 3dg file #20

Open DS57 opened 5 years ago

DS57 commented 5 years ago

Hi @tanlongzhi

I have processed single cell data using the hickit pipeline. After phase imputation I was able to generate the 3dg file. Now that I try to convert this 3dg file into a cif file (for viewing in pymol), it gives me the following error.

Error_hickit_screenshot 1

Is there an alternate method to visualize a 3dg file directly?

Thank you for your help.

Divyaa

tanlongzhi commented 5 years ago

Hi @DS57, Have you converted your hickit 3dg file into a dip-c 3dg format beforehand? It can be done with a script supplied with dip-c:

scripts/hickit_3dg_to_3dg_rescale_unit.sh in.3dg

This will generate a dip-c 3dg file in.dip-c.3dg for further conversion into mmCIF. Note that the above only works with more recent versions of hickit (with #unit header), to be released as v0.1.1.

DS57 commented 5 years ago

Hi @tanlongzhi

Perfect! I will try this. Thank you so much.

Divyaa