No preset with name "kAligner2".

[Angieiscute]

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!

[mizraelson]

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.

[Angieiscute]

oh, I recalled, it should be -MreadsLayout=Collinear \

[mizraelson]

Collinear is required if both of your reads are either forward or reverse. If your R1 is forward and R2 is reverse, you shouldn't use this parameter.

[Angieiscute]

I got u! Thanks!

[abspangler13]

Is this true for the smart-seq2-vdj preset? As in kAligner2 is the default.

[mizraelson]

Yes, kALigner2 is now used in all presets.