single-cell-genetics / singlecell_neuroseq_paper Goto Github PK

Hi,

I’m a researcher at the LMB in Cambridge and we are interested in running your neuronal differentiation prediction model on additional datasets.

The Jupyter notebook is fine to run, but I had queries about how to quantitate the RNA-seq data prior to running your classifier. For example, my own RNA-seq quantitation pipeline does not output all the genes used in your model, which I suspect is a result of using a slightly different genome annotation.

Is there a protocol to follow with regards to the bioinformatic processing of the RNA-seq data. Sorry if I have missed something obvious in your paper or GitHub description.

Many thanks for your help.

All the best,
Steven