Extracting internal reads from SmartSeq3 data using zUMIs
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7 weeks ago
pm2012 ▴ 110

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.

internal UMI zUMIs reads SmartSeq3 • 97 views
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