Question about --glitches

[riccardo-aiese]

Hello,
thank you very nice for this nice tool! I am working on the analysis of repeat expansions in few human genes from different patients. Basically we amplify a target region containing some repetitive elements and then we sequence with Nanopore in order to estimate the length of the repetitive elements. Each patient has a different length of the repetitive elements which should appear with the analysis of the Nanopore data.

I am trying to use Badread in order to simulate reads from the same amplicon regions in order to evaluate how well we can estimate the repetitive content using a controlled dataset. I would like to know what is your recommendation for the "glitches" parameter. I noticed that in the help you suggested the settings for the "identity" parameter for an OK run, could you do provide the same suggestion for the "glitches" parameter? Is there a way to estimate the best settings starting from my own sequencing data in order to simulate reads which are very close to my real data?

Thank you very much for your support,
Riccardo