Trimming Necessity Before MiXCR v3.0.13 Alignment for SMARTer Human TCR Profiling in RNAseq data with some issues in report fastqc file ?

[HV28]

Hello everyone,

I am working with RNA-seq data generated using the SMARTer Human TCR α/β Profiling Kit. Some of my samples show issues with adapter content and/or low Phred scores (<20-25) at the longer read lengths.

I need to align my data with the version 3.0.13 to ensure compatibility with previously analyzed samples. Before running MiXCR alignment with -rna seq preset option, would you recommend performing a trimming step to remove adapters and low-quality bases, or does MiXCR internally handle these issues effectively?
If trimming is recommended, is there a quality score threshold below which it becomes necessary?

Thank you in advance for your insights and for the quality of the documentation provided for MiXCR—it's greatly appreciated!

[mizraelson]

Generally speaking, there is usually no need for any extra preprocessing. Also, you should use the following command for this kit and mixcr v3.0.13 (not the RNA-seq preset, as this is an amplicon-based protocol):

mixcr analyze amplicon \
--species hsa \
--starting-material rna \
--5-end v-primers \
--3-end c-primers \
--adapters adapters-present \
input_R1.fastq.gz \
input_R2.fastq.gz \
result

However, I strongly advise using the latest version and reanalyzing your previous samples with it as well. There are a huge number of enhancements compared to v3.0.13.