Ampliconの場合

mixcr \

analyze \

amplicon \

--species hs \ # species(hsa; human, mmu; mouse, rat)

--starting-material dna \ # dna or rna

--5-end v-primers \ # no-v-primers(switching oligo etc) v-primers(v primers)

--3-end j-primers \ #j-c-intron-primers #j-primers #c-primers

--adapters adapters-present \ #adapters-present(may be present) #no-adapters

input_R1.fastq \ #read 1

input_R2.fastq \ #read 2

analysis #output

Shotgunの場合

mixcr \

analyze \

shotgun \

-s <species> \

--starting-material <startingMaterial> \

input_file1 \

[input_file2] \

analysis_name