Option to not use preset

[ninaxiong11]

I am analyzing data sequenced on a custom panel that does not belong to any of the built-in presets. Previously I have run analyses using MiXCR version 3.0.10 and did not have to specify any preset. However, when I run the same analyses using the latest MiXCR version, I have to use a preset. I tried using various presets including exome-seq and generic-amplicon but was not able to identify any clones. Is there an option to not specify any preset?

[mizraelson]

Hi,
Can you specify which wet-lab protocol you use? Is there a published? What commands did you use with v3?

Sincerely,
Mark

[ninaxiong11]

Hi Mark,

Because it's a custom panel, there is no published protocol. Cell-free DNA was extracted from blood plasma, and sequencing libraries were constructed using UMIs and xGen duplex sequencing adapters with dual index barcodes. I used align, assemble, and export with v3.

[mizraelson]

The latest MiXCR can handle UMIs. Can you tell me more about the library structure?
• Where is the UMI located in the read? How long is the UMI? Is it at the very beginning of the read?
• What reagan do you cover? Only CDR3?