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The question about using MIXCR to analysis RNA-seq data

#1

I download some RNA-seq data on NCBI, Include lung cancer tissue and adjacent normal tissue data for the same person.
The first question:
The difference in the types of TCR/BCR between cancer tissues and adjacent tissues is particularly large.What is the cause of this? Is it normal?

The second question:
This is my command：
mixcr align -p rna-seq -OallowPartialAlignments=true -OvParameters.geneFeatureToAlign=VTranscript SRR4296${i}_1.fastq.gz SRR4296${i}_2.fastq.gz SRR4296${i}_paired.vdjca
mixcr assemblePartial SRR4296${i}_paired.vdjca SRR4296${i}_paired_rescued_1.vdjca
mixcr assemblePartial SRR4296${i}_paired_rescued_1.vdjca SRR4296${i}_paired_rescued_2.vdjca
mixcr extendAlignments SRR4296${i}_paired_rescued_2.vdjca SRR4296${i}_paired_rescued_2_extended.vdjca
mixcr assemble -ObadQualityThreshold=0 SRR4296${i}_paired_rescued_2_extended.vdjca SRR4296${i}_paired_rescued_2_extended.clns
mixcr exportClones -c TRD SRR4296${i}_paired_rescued_2_extended.clns SRR4296${i}_paired_rescued_2_extended.clns.txt
I want to analyze RNA-seq data，and extract the TCR’s TRD chain. But TRA will appear with TRD. What is the reason?
Thank you very much !

#2

TRD and TRA are the same genetic locus and some V segments can be utilized in both rearrangements types. Could this be an explanation?

#3

Hi, since MiXCR series 4 it’s possible to distinguish TRA and TRD based on C gene sequence if it’s covered by the reads. Also now we introduced a specific preset for rnaseq data so it’s possible to run the analysis in a one line command.

Please see our new documentation portal:
https://docs.milaboratories.com/mixcr/guides/rnaseq/