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mtisza1 / Cenote-Taker2

Cenote-Taker2: Discover and Annotate Divergent Viral Contigs (Please use Cenote-Taker 3 instead)
MIT License
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ITR length and running irf #26

Closed eul2021 closed 1 year ago

eul2021 commented 2 years ago

Hi Mike,

  1. I was wondering if there's any limitation on contig length to detect ITRs? For instance, in your test contig example you're showing a relatively short ITR. What if my ITR is > 100bp? Any parameters to irf input I should adjust?

  2. If I want to debug irf module by itself - how would you recommend to run it? I tried just invoking the executable, but it doesn't work. It seems to work from within cenote, though, as no error message in the output is found.

Thank you very much for your help.

mtisza1 commented 2 years ago

Hi eul2021,

  1. I honestly don't know the length limit, but it should be over 100 nt. The irf tool is quite old and the documentation is kind of difficult to interpret: link
  2. Are you running irf and Cenote-Taker 2 in linux? you should just be able to do this command:

./irf307.linux.exe

Let me know if you have any more trouble and what you find out about length limits on ITRs.

Mike

eul2021 commented 2 years ago

Thank you, Mike! I managed to run the irf and now my ITR contigs are detected correctly. Thank you for your help.

mtisza1 commented 2 years ago

OK, sounds good. If there was something sub-optimal about how irf was being implemented in the tool, please let me know.

Mike