Dear Kneaddata developers,
I would like to know more details about the TRF option in Kneaddata: why is it necessary to use TRF? And is it suggested to run kneaddata with TRF? I tried to find out the answer by looking at the manuscript for kneaddata, but it says “TBA” on the github repo. Many thanks!
Thank you for reaching out to the biobakery Lab.
You can find a bit more about TRF parameters in the Kneaddata Tutorials below:
I will add more details on the TRF in the User manual as well. Thank you for the suggestion.
Thank you for the information! I check the updated Github page and still have one question left: Is it suggested to run the trf in kneaddata? In other work, which situation is necessary to run trf?
I notice the wiki says the trf does not run by default, but I never had to specify --run-trf argument and I can always see it did run in my logs. Has it been switched on to default in later versions ? If so, you must believe it is more necessary than not. I would also like to know what warrants removing tandem repeats.
I am assuming the tandem repeats are being removed in the same manner trimmomatic works, i-e trimming the entire read from where it finds a hit ?