How to use the extra args?

[Yang990-sys]

My requirement is to make fast5 include fastq and trace table. By looking up the instructions, I understand that the fast5_out should be set out to True. Which of the following expression is correct in syntax?

extra_args=["--fast5_out=True"]
extra_args=["fast5_out=True"]
extra_args=["fast5_out=on"]
extra_args=["--fast5_out=on"]
extra_args=["--fast5_out"]

extra_args would be passed to protocol_args.extend(args).

I have failed many times . I would appreciate your help.

[0x55555555]

Hello!

If you are using our supplied tools to start a protocol: https://github.com/nanoporetech/minknow_api/blob/master/python/minknow_api/tools/protocols.py#L350 you shouldnt need to use the extra args, instead just pass

We have an example which turns on your required output here: https://github.com/nanoporetech/minknow_api/blob/master/python/minknow_api/examples/start_protocol.py

You could run the above example using --fast5 and --fastq to write these file types.

Thanks,

• George

[Yang990-sys]

Thank you for your suggestion! But the fisrt step I have tried is --fast5 and --fastq. Disappointingly, this step did not work . My fast5 file has no Analyses Group which should contain fastq and trace table. My minknow is v5.3 and guppy is v6.0.

[0x55555555]

Hi @Yang990-sys ,

More modern versions of minknow do not write analysis sections to fast5 files - this is not possible via the UI or the API.

Whats your use case for the fast5 file containing the fastq + trace data?

Thanks,

• George

[Yang990-sys]

Hello,

My goal is to measure the polyA length of cdna in large quantities using tailfindr or PolyACaller with SQK-PCS111, both of which require a trace table. Rebasecalling with stand-alone guppy6 would wastes a lot of resources and time. So is there a better solution? Is it feasible by specifying the basecall config file in the API ?