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ma-compbio / Higashi

single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph
MIT License
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scTAD calling #7

Closed tarak77 closed 3 years ago

tarak77 commented 3 years ago

Hey @ruochiz , I am trying to call TADs and compartments on my imputed maps at 1mb resolution. In the scTAD.py code, I use -n --window_ins 1000000 --window_tad 1000000.

Although the wiki says that

When including --neighbor or -n, the algorithm will call TADs on the imputed contact maps with neighboring cells' information utilized.

I get the error:

usage: scTAD.py [-h] [-c CONFIG] [-n NEIGHBOR] [--window_ins WINDOW_INS]
                [--window_tad WINDOW_TAD]
scTAD.py: error: argument -n/--neighbor: expected one argument

Also when I explicitly specify -n 5 the same as what I give "neighbor_num":5 in json file....I get the following error:

unable to open *_nbr_1_impute.hdf5

Any help will be great!!

Your TAD/compartments result figures are really useful and awesome!! Is there a tutorial available to create figures like those?

ruochiz commented 3 years ago

For future reader of this issue: the bug has been fixed. The -n without inputing number should be the correct way of using the script.