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Suppose I ran mixcr align with a tag pattern like this:
(CELL:N{8})(UMI:N{8})gcgcg(R1:*)atatatat
Is there a way to export the extracted R1 sequence and qualities?
I tried
mixcr exportAlignments -f -targetSequences -targetQualities test.vdjca > test.alignments.tsv
.I wasn't sure if there is any additional processing was done to R1, and whether it is equivalent to "targetSequence" in this context.
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