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Hi! Thanks for developing this great tool! I have a very similar problem. We sequenced 5' scRNA-seq with Biolegend TotalSeq C hash tags and I get 100% unmapped. However, the...

Thanks for the quick reply. I double checked and it does not seem to be the case. Here are the first two lines of the grep output: ACCCACCAGTAAGAC ACCCACCAGTAAGAC