Double UMI

[Absent98]

Hello, I just started with the computational analysis on different formats of Rep-Seq libraries that I've built on my own (without commercial kits), and I'm struggling to find the correct pipeline/preset that can suit my type of data. I have two main concerns:

• can mixcr manage long single-end reads with double UMIs, also for error correction of course ? (aka reads with molecular barcodes on both ends of each read)
• If I have a non-human multiplex amplicon-library targeting just the CDR-H3 -alongside the flanking V and J regions - can I analyze it properly?
  Thank you in advance for your help !

[mizraelson]

Hi,
yes MiXCR can handle all kinds of custom libraries. You would need to use a generic preset and define the read structure with UMIs using --tag-pattern

[Absent98]

Thank you very much for your prompt reply !