Dear all,
Previously I have used kallisto and sleuth to analyse bacterial bulk paried-end RNA-seq data from Truseq library preparations. We are now trying to optimize and tailor our approach and used a Lexogen CORALL total RNA-Seq library preparation with N12 UMIs to deduplicate PCR duplicates.
Do you know a good way of doing UMI extraction and UMI deduplication in a kallisto pipeline with bulk paried-end RNA-Seq data?
Kind regards,
Janine