UMI

[PavithraV0223]

Checklist before submitting the issue:

• The issue is strongly related to the MiXCR software
• The issue can be reproduced with the most recent version of MiXCR
• There is no answer to the question in the official documentation and there is no duplicate issue in the bug tracker
• Inspection of raw alignments with exportAlignmentsPretty shows that data has the expected architecture, and sample preparation artefacts are not the reason of the problem (if this is the matter of the issue)

Expected Result

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Actual Result

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Exact MiXCR commands

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MiXCR report files

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[mizraelson]

Hi. Nanopore sequencing is usually unoriended, which means UMI can be on either end of the read. Can you share the library structure (are there any barcode sequences present that we can use as an anchor) and maybe a file with a few reads so I can adjust the pattern?

Sincerely,
Mark

[mizraelson]

Sorry for the delay.
Please try the command bellow:

mixcr analyze generic-ont-with-umi \
	--species lamaGlama \
	--tag-pattern "^*CTTCCGATCT(UMI:N{12})N{5}(R1:*)" \
	-Malign.tagUnstranded=true \
	data.fastq \
	output

Let me know how it worked.

Sincerely,
Mark

[PavithraV0223]

Thank you, It did work