Output about mixcr HOT 4 CLOSED

The determination process is somewhat more complex than simply examining the number of reads. Initially, the sequencing quality of the nucleotide is considered. Subsequently, a negative binomial distribution is applied to ascertain if this nucleotide might be the result of an error, accounting for both the read proportion of the clones and the quality of the sequencing.

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Hi,
Could you please provide the exact command you used?

To address your question, we should initially examine the alignments that support each clone. This can be done using the mixcr exportAlignments input.vdjca output.tsv command. It's likely that there was a comparable number of reads supporting each variant, cause clustering only happens if one clone has a significantly lower count.

Sincerely,
Mark

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I basically used generic-amplicon preset set-ups and made only changes during exportClone parameters (I believe generic-amplicon by default clusters by CDR3 sequences with max mutations allowed being 2 nt mismatches or 1 indels but not both).

from mixcr.

I was wondering since these clonotypes have identical CDR3 seq (with 1 difference in nt) and also identical V and J segments, does it make sense to combine or cluster these clonotypes together?

The read count comparison is 284 vs 5. What is the threshold for valid number of reads that support each variant?

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