Tag for MIXCR on ONT and 10x reads

[lauratwomey]

Hi, thanks so much for the great tool & documentation!

I'm trying to run MIXCR on a fastq file sequenced with Nanopore. However, the original library was a 10x library - following Chromium Next Gem single cell 5' structure.

I've attempted running:

mixcr analyze generic-ont-with-umi \
    --species hsa \
	--tag-pattern "^(CELL:N{16})(UMI:N{10})(R1:*)" \
	$INPUT \
	Sample_multisample

It seems to finish the alignment step but fails at refineTagsAndSort

�[31m�[1mCaused by: java.lang.IllegalArgumentException: Unexpected filter tag request. Requested UMI but next level is CELL.�[21m�[39m�[0m
�[3m	at com.milaboratory.o.gn$b.getKeyExtractor(SourceFile:957)�[23m�[0m
�[3m	at com.milaboratory.mitool.refinement.gfilter.KeyedFilterContext.getKeyExtractor(SourceFile:97)�[23m�[0m
�[3m	at com.milaboratory.mitool.refinement.gfilter.GroupFilter.filter(SourceFile:297)�[23m�[0m
�[3m	at com.milaboratory.o.gn.g(SourceFile:654)�[23m�[0m
�[3m	at com.milaboratory.o.gn.c(SourceFile:473)�[23m�[0m
�[3m	at com.milaboratory.mixcr.cli.CommandRefineTagsAndSort$Cmd.run1(SourceFile:373)�[23m�[0m
�[3m	... 26 more�[23m�[0m

I'm unsure whether that is the right pattern to use in this case or if the error is due to a different cause. Any help greatly appreciated!

[mizraelson]

Hi, the generic-ont-with-umi preset does not support CELL barcodes. You can use the custom preset from this discussion #1681