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- First Release - February 2018
3DMax allows two formats:
- Tuple Input format(preferred) : A hi-C contact file, each line contains 3 numbers (separated by a space) of a contact, position_1 position_2 interaction_frequencies
- Square Matrix Input format: The square matrix is a comma seperated N by N intra-chromosomal contact matrix derived from Hi-C data, where N is the number of equal-sized regions of a chromosome.
Output: there are 4 files:
- .pdb: contains the model and can be visualized by pyMol, Chimera or GenomeFlow
- _log_a_number.txt: contains the settings used to build the model and Spearman's correlation of reconstructed distances and input IFs
- .log.txt: NUM > 1, the files contains settings and average root means square error (RMSE) and average correlation of Spearman's and Pearson's correlations of separate models
- _coordinate_mapping.txt: contains the mapping of genomic positions to indices in the model. Notice that indices start from 0, while in pyMol or Chimera, id starts from 1