Akanksha2511

Hi, Sorry about the issue. Can you please share few lines of the nanopolish input file you used? Also, we recommend using the C++ version for faster preprocessing. Thanks, Akanksha

Thanks, the format for nanopolish file looks ok. Can you please try 2 things: 1) run the preprocessing code on the test file (https://github.com/comprna/CHEUI/blob/master/test/nanopolish_output_test.txt) to see if the installation is...

Thank you so much for running the 2 tests. Do you get the error message after some temp files are created or its straight away? We can look at our...

Thanks. Just wondering is it possible to run the script without multiprocessing (n=1). Also can you please share the number of lines in your nanopolish file. Thanks, Akanksha

Thanks. Yes running in background should be fine. I think it gets stuck somewhere between line 253500000 to end of your file which is 254747839. Can you please cp the...

Also if you can share the output file that you got from the above run might be useful. Thanks, Akanksha

Hi, Sorry about the delay in reply. So if you look at last two lines of your file they look weird. ``` 1747834 gene9 616.0 GCTGA c9ee63a7-28b7-40a9-a743-c0eccfba7f73 t 127.0 81.03...

Hi, If it says "All signals have been processed" that means its complete. To get the position of the center nucleotide you need to add +5. The position column gives...

Hi, Yes, the second column in the read_level_prediction_m6A_sorted will provide the read-level prediction probability from model 1. Then we have model 2 that takes those probabilities and predicts site-level probabilities....

Hi Sukriti, The position is the position of the first nucleotide in the site column. So for example below ``` contig position site coverage stoichiometry probability ENST00000000233.10 1003 CTTGAGTAA 648...