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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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read length #22

Closed rberrens closed 5 years ago

rberrens commented 5 years ago

Is there a possibility to not change the read length but just give the deepsimulator a fasta file with different sequences and only model the errors without changing the length of the sequences?

liyu95 commented 5 years ago

Hi, thank you very much for your interest!

Yes, that's possible and that's exactly what we want to achieve. You can start from the second step of our three-step pipeline, as illustrated in the figure here: https://github.com/lykaust15/DeepSimulator/blob/master/example/main_graph_wsmod3.png.

You just need to modify the file 'deep_simulator.sh'. If you find the file is hard to modify because we have added some many parameters to it. You can use 'main.sh', which is more intuitive to understand than the 'deep_simulator.sh' file.

Feel feel to let us know if you have more questions.

liyu95 commented 5 years ago

Hi, we have issued a major update to DeepSimulator, please refer 'case_study.sh' for the three-step pipeline of our tool.