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liulab-dfci / TRUST4

TCR and BCR assembly from RNA-seq data
MIT License
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TCR CPK and clonality #159

Closed jhylwq123 closed 1 year ago

jhylwq123 commented 1 year ago

Thank you for developing this tool ! When I used trust-stats.py to calculate the CPK and clonality based on the report.tsv, I found it reported CPK and clonality for TRB and TRA seperately. My question is if I want to calculate the CPK and clonality for the TCR, is it simply add TRA and TRB together?

mourisl commented 1 year ago

They should be regarded separately. I would recommend using TRB's CPK and clonality. This is because TRB chains tend to have higher expression than TRAs, and TRUST4 can recover more CDR3s and the statistics are more reliable.

jhylwq123 commented 1 year ago

Got it, thanks for your advice!