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I think that the library preparation is more critical than the sequencing machine. If the preparation was different, since each method has its biases, the comparison is not valid.
thank you for a replay.you mean I should investigate their library preparation ?
Yes, exactly. If they're public it's more problematic.
Hello, Could you please tell me whether different datesets generated by multiplex PCR and 5'UMI-tagged 5′-RACE can be analyzed together? The sequence depth is different varying from each other so the abundace analysis seems very comparable. But I am afraid that such difference is caused by differnt sequence methods and platforms. What can I do to normalize these datesets or how can I intergrate these datesets? Could you please give me some suggestions and instructions on how to normalize TCR-seq data? I really need your help!!! Looking forward to your reply. Thanks and best regards, Linqy