Flower9618

trimming adapter about bonito

2

Hi, I just would like to know whether guppy or bonito will trim adapter during the basecalling process? If yes, we would like to know whether it is by default...

'Aborted (core dumped)' when running 'bonito evaluate' command

2

Hi, When I try to use 'bonito evaluate' command to evaluate the model trained using my own data, there is an error: And when I run the same 'bonito evaluate'...

question about 'bonito train'

4

Hello, I am trying to train my model using my own data. But there is an error "RuntimeError: target_lengths must be of size batch_size". Attached is the screenshot of the...

Hello, I would like to know why we need to trim the raw signal using 'trim_start' and 'trim_end' these two parameters, and how to select the suitable value for these...

question about 'flipflop_remap'

2

Hello, thank you very much for providing this useful tool. I just have a question when I read the code in https://github.com/nanoporetech/taiyaki/blob/9672c66d654ad8101c4faf481646493082e090c8/taiyaki/flipflop_remap.py#L123 Why K=2*nbase*(nbase+1)? and waht does T mean?

tombo resquiggle for r10 data

1

Hi, Thank you very much for this very useful tool. I am very interested in this tool. I just would like to know whether tombo can be used for nanopore...

The performance for the long read, and comparison with porechop

5

Hi, thank you very much for sharing this tool. I would like to know two questions: 1. what is the difference between cutadapt and porechop, which is another adapter trimming...

Hi, thank you so much for sharing this useful tool. When I run guppy to do the base modification by using '...modbase.cfg' of guppy and require the .bam out. I...