Amplicon reads simulation

[MaestSi]

Dear DeepSimulator developers, I would like to use your tool for simulating nanopore reads, resulting from amplicon sequencing. However, all the reads in pass.fastq have exactly the same errors. Are there any parameters that I am missing? I tried both the context dependent and context independent pore models, but the results were very similar. Moreover, when I set-n -1, it looks like the -K parameter value has no effect, since one single read is produced instead of K reads. Thanks in advance, Simone

[MaestSi]

I realised that performing a for loop and setting a different -S value at each iteration does the job. For example: for f in {1..10}; do ./deep_simulator.sh -i template_reference.fasta -B 2 -n -1 -S $f -o "template_reference_DeepSimu_"$f; done generates 10 amplicon-like reads. Let me know if there are better solutions, or if this one should be ok. Thanks, Simone

[liyu95]

Hi Simone:

Yes, I think that's a reasonable solution to your problem. -S is used to control random seed, which can introduce different errors to different sequences.

Sincerely, Yu

[MaestSi]

Thank you very much, Simone