Comparing 5'RACE TCR Sequencing Methods

Question

[tdfyoder]

Hello,

My laboratory developed an in-house 5'RACE method with custom primers targeting the constant region of the gamma/delta T cells. We submitted RNA to a third party commercial laboratory to benchmark our method against their 5'RACE method. Both our in-house fastq's and the third party's were processed using MiXCR. How legitimate is it to compare clones from the different library prep methods in a longitudinal analysis (more time points were captured in the in-house method than were submitted to the third party)? Thanks!

Answer 1

[mizraelson]

Hi, different methods can lead to different results thus I would recommend work with these datasets separately. But you should see some major differences and likelihoods if the are there even if you join the datasets. Also, how different are the two methods? is the difference only in C gene primers? does any of the two use UMIs?