single cell

First, demultiplex your data given a sample sheet:

cellranger  mkfastq --run RAWDATA_DIRECTORY/ --csv SampleSheet.csv  --id TEST 

e.g.:

Lane,Sample,Index
*,A,SI-TT-A8
*,B,SI-TT-A9
*,C,SI-TT-A10
*,D,SI-TT-A11

the * means merge the lanes

We then need a mapping ref:

curl -O https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-and-mm10-2020-A.tar.gz

before counting the reads:

cellranger count --transcriptome refdata-gex-GRCh38-and-mm10-2020-A --fastqs TEST/outs/fastq_path/AACKTYTM5/ \
      --localcores 4 --localmem 64 --id count_output --sample A,B,C,D