Specifying Read Numbers and Using Badread Models

[zzare-umd]

Hi,

Thank you for the excellent tool for simulating long reads! I'm using TKSM to simulate PacBio reads and have a couple of questions:

How can I specify the exact number of reads I want to simulate?
I noticed that you recommend using the pacbio2016 error and quality model from Badread for simulating PacBio RS II reads. However, Badread now includes a pacbio2021 model for PacBio HiFi reads. Is it possible to use this model in TKSM for HiFi read simulation?

Best regards,
Zahra

[f0t1h]

Hi Zahra,

You can set the number of reads with the '--molecule-count' option with the transcribe module.

While we did not test it, new Badread models should be usable with TKSM. Please let us know if something comes up.

Best,
Fatih

[baraaorabi]

Just to add to Fatih's answer, the final number of reads is determined by the number of molecules in the MDF file output by the final module used before the Sequencing module. The two main modules that affect that count are:

• Transcribe module: --molecule-count will determine how many molecules are generated from the expression profile.
• PCR module: --molecule-count will determine how many molecules are captured by PCR after the amplification cycles. Typically, this is the number that will correspond to the final number of reads.

Cheers,
Baraa