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GuipengLi / ChIA-PET2

a versatile and flexible pipeline for analysing different variants of ChIA-PET data
GNU General Public License v3.0
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bug in trimLinker -h #20

Open fengpku opened 5 years ago

fengpku commented 5 years ago

when type > trimLinker -h not only print the help page but also print: Wrong parameters

thought it is not a big issue

fengpku commented 5 years ago

Two more questions:

  1. -l min length of timmed reads: default=15 should be trimmed
  2. what is the function of -k keep empty

Thanks!

GuipengLi commented 5 years ago

Thank you for reporting these. The "-k" parameter control what kinds of read pairs are kept for sequential analysis. It basically check if the reads containing the linker sequence.

-k|--keepempty: 0,1,2; 0:No linker-empty reads; 1:keep 1 linker-empty read; 2:keep 2 linker-empty reads.

41622236 commented 3 years ago

Hi,

I am analysing ChIA-PET data using ChIA-PET2 tool. I wanted to know what exactly the following terms mean from the trim statistics the tool provides:

Expect PETs Expect both PETs

What is the difference between Expected and Expected both PETs? None of the information is provided in the tool paper. Any help would be appreciated. Thanks!