Extracting internal reads from SmartSeq3 data using zUMIs

Question

[pm2012]

Hi,

I am using the zUMIs pipeline to analyze SmartSeq3 data. I am looking for a way to extract the internal reads and map them separately from the UMI reads to get their genomic distribution across regions (introns, exons etc). How can I do this either using zUMIs or other tools? I am thinking a pattern search of 11bp tag present in the UMI containing read might be helpful here. Any suggestions are highly appreciated.