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AveSim is a pipeline to simulate Hi-C matrices involving CNVs and translocations.
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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. _____________________________________________________________________ Contact firstname.lastname@example.org (Abhijit Chakraborty)