Closed tjprins closed 1 year ago
hi @tjprins, sorry for the delay in my response. Thanks a lot for your feedback, especially the --infer_mod_rate command which I was sure I had already fixed but must be somehow overwritten. I've just fixed it after reading this, thanks a lot for bringing this to my attention. As for your questions:
Anyway thanks for including m6Anet in your m6A detection protocol. Let me know if you have more questions / feedbacks and I will try to respond to them as soon as I can
Best Regards
Christopher Hendra
Awesome, thank you for your response! I have a few more general questions then:
--disable_qscore_filtering
option enabled. For m6ANet, would you recommend disabling qscore filtering of reads? Or just run m6ANet on "pass" reads?probability_modified
column, which can be relaxed at the expense of having lower model precision." I'm curious how that threshold was determined? mod_ratio
vs. probability_modified
? Based upon your paper and the documentation, I presume that the mod_ratio
is the percentage of reads that were determined to have a modification with the probability specified by probability_modified
, but is it possible to have a high mod probability and low mod ratio? Do you think it should be normalized in some fashion?Thanks for all your help!!
Hi @tjprins,
Thank you for the questions, I am converting this issue into discussion since it feels more like a discussion at this point. But to answer your questions:
Hello, really looking forward to giving this a try with our lab's dataset. Detecting m6A modifications has been quite a challenge to get up and running, but m6Anet looks like a great alternative to other already established methods.
After getting things setup, I just have a few questions. I'm pretty sure I know the answer to these, but I just want to verify:
Also, a little feedback:
m6anet-run_inference --input_dir demo_data --out_dir demo_data --infer_mod-rate --n_processes 4
contains a typo.--infer_mod-rate
should actually be--infer_mod_rate
, otherwise it throws an error.conda create --name m6anet
) prior to the install which fixed the issue.Thank you so much!