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ay-lab / HiCtrans

HiCtrans is a pipeline to call translocations from Hi-C data
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The instruction is not clear about the input data in calculating the whole genome translocation site #1

Closed ChenFengling closed 6 years ago

ChenFengling commented 6 years ago

Could you put a whole genome test data.? I'm really unsure about how should I organize my data in whole genome option.

abhijitcbio commented 6 years ago

The whole genome test data is too large and can't be uploaded, but please follow the instructions below to run the script

  1. Create an "input.txt" file inside "Translocation_calling" folder

  2. In the input.txt write the following lines

Genome.bed Genome.matrix all all

Genome.bed is the full genome bed file with index information similar to T47D.chr7_15.bed file (default 40Kb resolution). Genome.matrix is the full genome raw Hi-C data in sparse matrix format similar to T47D.chr7_15.matrix file (default 40Kb resolution).

  1. Copy your bed and matrix file inside "Translocation_calling" folder.

  2. Run HiCtrans with the following command

perl run_HiCtrans.pl input.txt (This will create the bash file to run the job)

Note: HiCtrans requires a restriction enzyme specific genome feature file with GC content, mappability information for translocation detection. By default hg19 HindIII restriction enzyme specific file @40Kb resolution is provided.

ChenFengling commented 6 years ago

THX! It works well. I think it should also be mentioned in the document that the idx is made across the whole genome from 1.

abhijitcbio commented 6 years ago

Thanks for the suggestion. Added.