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milaboratory / mixcr

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.

Home Page:https://mixcr.com

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No preset with name "kAligner2".

Angieiscute opened this issue · comments

commented

Hi,

App version: 4.5.0;

When I employ the following command:
mixcr align --rna --preset generic-bcr-amplicon --species hsa
A warning is raised:

WARNING: Preset generic-bcr-amplicon is deprecated. The preset is deprecated. Please use generic-amplicon.

Subsequently, I attempted to utilize:

mixcr align --rna --preset generic-amplicon --preset kAligner2 --species hsa

This resulted in an error:

option '--preset' (<preset>) should be specified only once.

Hence, if I want to apply kAligner2 for BCR analysis, what are the correct options to use?

Thanks!

commented

We have updated our kAligner2 to accommodate both TCR and BCR data. As a result, we have replaced generic-bcr-amplicon and generic-tcr-amplicon with generic-amplicon. So there is no need to specify kAligner2 separately.