ReadMe.txt

AveSim is a pipeline to simulate Hi-C matrices involving CNVs and translocations. AveSim can perform the simulation at the restriction site resolution level (RE_level_simulation folder) or at fixed-size bin resolution level (Fixed_size_simulation folder).

RE_level_simulation folder is subdivided into following subfolder A. Amplification > scripts > simulation B. Deletion > scripts > simulation C. Translocation > scripts > simulation D. DoubleMinute > scripts > simulation

Users can generate the simulated paired-end fastq files in the simulation folder. These fastq files can be processed by any standard Hi-C data processing pipeline.

Fixed_size_simulation folder is subvidived into following subfolder A. data B. InputFiles C. TranslocationScripts D. Non-Reciprocal_Balanced_Translocation E. Reciprocal_Balanced_Translocation
F. Unbalanced_Translocation

Users can perform different translocation simulations (D,E and F) under the respective simulation directories. Fixed-size simulation will create 2D Hi-C matrices.

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Contact

abhijit@lji.org (Abhijit Chakraborty)