kallisto UMI deduplication with bulk paired-end RNA Seq

[Janine Lux]

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. 

So far, the analysis pipelines I found (e.g. https://github.com/Lexogen-Tools/corall_analysis) don't use kallisto. 

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