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s175573 / GIANA

Ultrafast TCR clustering algorithm based on geometric isometry
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query TCR that are similar to rare reference TCRs #7

Open shuailinli opened 1 year ago

shuailinli commented 1 year ago

Hi Dr. Li,

Thanks for your nice paper and tools for clustering TCR sequencing, it is really helpful. I just have a naive question. When you query new TCR-seq samples against existing reference, you mentioned that there are query TCR that are similar to rare reference TCRs so that in such case a query cluster did not contain any sequence in the reference cluster. In figure 3c of you NC paper, you mentioned "For each query sample, we calculated the fraction of TCRs co-clustered with COVID-19 reference patients.". I just want to know that if the query TCR is clustered with a rare COVID-19 reference TCR that are not in the COVID-19 reference cluster, do you count it as co-clustered with COVID-19 reference patients.? Or a query TCR has to be clustered with a COVID-19 reference cluster to be called co-clustered with COVID-19 reference patients.

Thank you!

s175573 commented 1 year ago

Both rare and previously clustered TCRs will be taken into account. The use of reference cluster is to eliminate the need of clustering the reference TCRs again.