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liyu95 / DeepSimulator

The first deep learning based Nanopore simulator which can simulate the process of Nanopore sequencing.
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Bug in checking accuracy #41

Closed renzilin closed 4 years ago

renzilin commented 4 years ago

Hey, I was using your deepsimulator to generate some fast5 files with deep_simulator.sh Here is the cmd line $DS/deep_simulator.sh -i fasta/th01_editted/th01_0.fasta -n 200 -S 110 -B 2 -M 0 -o simu_fast5/th01 -H $DS The DS is the full path where the software located. I used -H to make sure the minimap2 work.

However, there is a bug. image I though it was because the sh script can't find the minimap2, but after I added the minimap path by -H, it still shows the error.

Best, Zilin

renzilin commented 4 years ago

Besides that. If there are several reads in the template fasta file, will the DeepSimulator generate NUM_OF_TEMPLATES * NUM_OF_SIMULATED_READ reads ? Thank you!

liyu95 commented 4 years ago

Hi, thank you very much for your interest! Could you please check whether you get the same bug on the example we provided?

renzilin commented 4 years ago

Dear Yu, Thanks for your help. I found the template fasta sequence I provide may cause the both problems I put on github issues. The template is too short (201 bp) to introduce the noise into the signal if I use the default signal std and event std.

Thank you again.

Best, Zilin

On Sat, 27 Jun 2020 at 06:11, Yu Li notifications@github.com wrote:

Hi, thank you very much for your interest! Could you please check whether you get the same bug on the example we provided?

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