File | Date | Author | Commit |
---|---|---|---|
bin | 2016-07-25 | tuan | [a87e57] MOGEN source code |
documents | 2017-01-23 | tuan | [121a8e] add supplementary document |
examples | 2016-07-25 | tuan | [3a8ff6] remove file > 100 mb |
src | 2017-01-23 | tuan | [121a8e] add supplementary document |
LICENSE | unknown | ||
README.md | 2017-01-23 | tuan | [385445] add question 3 |
build.xml | 2017-03-10 | tuan | [07e31c] add buildfile |
Tuan Trieu
Department of Computer Science
University of Missouri, Columbia
Email: tuantrieu@mail.missouri.edu
Jianlin Cheng, PhD
Department of Computer Science
University of Missouri, Columbia
Email: chengji@missouri.edu
To run the tool, type: java -jar 3DGenorator.jar parameters_normal.txt
The file parameters_normal.txt contains parameters needed to run the tool
See in /examples/hiC/
for sample files
MOGEN produces two types of output files:
The executable software and the source code of MOGEN is distributed free of
charge as it is to any non-commercial users. The authors hold no liabilities to
the performance of the program.
MOGEN produces two output files, a .pdb file containing a model and a *_evaluation.txt file containing contact and non-contact scores of the model. Parameters are adjusted to maximize contact and non-contact scores. The effect of each parameter on corresponding contact and non-contact scores is mentioned in comments in the parameter sample file.
When there are multiple chromosomes, first, adjust parameters to have good contact and non-contact scores for chromosomes. Then, make sure that chromosomes don't intermingle by increasing inter, non-contact scores between chromosomes (> 60%). Next, let chromosome interacts at their border as much as possible but not intermingling significantly.
It's hard for all chromosomes to satisfy all these conditions, so, it is acceptable to have 1 or 2 chromosomes with low non-contact scores (small chromosomes, whose intra-chromosomal IFs are very strong) and 1 or 2 pairs of chromosomes that intermingle (again, small chromosomes as they co-localize in the center and their inter-chromosomal IFs are also strong). If chromosomes tends to intermingle significantly, try to reduce percentage of inter-chromosomal contacts.
This is because there is no or very few non-contacts in the input data, which often happens when the resolution is low (e.g 1MB). Set an appropriate contact threshold to make sure that there is at least 20% - 30% non-contacts (out of all possible contacts), the exact number doesn't matter because models are often similar.
If the thresholds are set as percentages (by appending % after the numbers), MOGEN will compute thresholds in interaction frequency (or contact count) and out the above message.