search

GoekeLab / m6anet

Detection of m6A from direct RNA-Seq data
https://m6anet.readthedocs.io/
MIT License
100 stars 17 forks source link

probability_modified and mod_ratio are 0 #168

Open lbwfff opened 3 days ago

lbwfff commented 3 days ago

Dear Developer

I was recently trying to analyze one of the HEK293T datasets using m6anet and I have some questions about the results. Some of the sites in the results file have 0 for both probability_modified and mod_ratio as shown in the figure below for example Screenshot 2024-07-05 at 12 58 35 PM , how should I interpret these sites.

Also, the maximum probability_modified in my results is only 0.35 and mod_ratio is 0.15 (data ERR4706156), which doesn't seem to be the expected result. Do you have any suggestions as to what is causing the low probability_modified and mod_ratio?

Thanks,

LeeLee

yuukiiwa commented 16 hours ago

Hi LeeLee (tagging you here @lbwfff),

Do you mind sharing the command you used to run m6anet inference, please? Also is your sample sequenced with RNA002 or RNA004?

Thanks!

Best wishes, Yuk Kei

lbwfff commented 12 hours ago

Hi Yuk, here are the parameters I used:

m6anet dataprep --eventalign /scratch/lb4489/project/dRNA/WT1_temp/ALL_eventalign.txt \
        --out_dir WT_1_m6anet \
        --n_processes 120

m6anet inference --input_dir WT_1_m6anet --out_dir WT_1_m6anet_result  --pretrained_model HEK293T_RNA004 --n_processes 120 --num_iterations 1000

The data source is from the xpore paper, so it should be RNA002