Bulk total RNA vs mRNA paired end sequencing data

[christoforos-dimitropoulos]

Hello,

I have some bulk sequencing data of sorted mouse CD4 T cells which I would like to import to mixcr. I have some fastq files (R1 and R2 for each sample,100nt each) and some samples were mRNA enriched before sequencing while others were not (total RNA was sequenced).
At the moment I am using:
mixcr analyze rna-seq
--species mmu
sample1_R1_001.fastq.gz
sample1_R2_001.fastq.gz
results/CD4
and I would like to acquire the TCR clones for each sample. Is this the correct way to do it? Any advice or tip would be appreciated :) Thanks a lot!

[mizraelson]

If this is a regular fragmented RNA-seq data, then the command is correct.