demultiplexing by multiple barcode positions about pheniqs HOT 1 CLOSED

Hi Simon

Thank you for using Pheniqs 😀

Pheniqs will not allow you to specify output directives on more than one decoder. That means you can't have it do exactly what you want in one step.

You can, however, achieve that in multiple steps. You can decode the first round of barcodes and break the output into multiple output files. Than further process the outputs in a second run.

Pheniqs is very fast making the two step process pretty efficient.

One of the reasons we picked json as the configuration file format is that it's easy to generate configuration files in python.

I think the fluidigm example does something like that.

The two step process is also more "statistically correct" since you can estimate the priors for each step from the data, giving you conditional, Bayesian, probabilities on a more specific dataset.

If you need a more concrete example, maybe you can provide a tiny example set and I can walk you through the configuration.

Lior.

from pheniqs.