cd ~
ln -s /share/biocore/workshops/2017_2018-single-cell-RNA-sequencing-Workshop-UCD_UCB_UCSF/ .
cd 2017_2018-single-cell-RNA-sequencing-Workshop-UCD_UCB_UCSF
cd 2017_10X_mouse_comparative/

module load cellranger
cellranger
cellranger mkfastq --help
cellranger count --help

ls -lah
less mkfastq.out
less mkfastq.err

cd cellranger-fastqs/
ls
cd HG27NBBXX
cd 654/

zless 654_S1_L008_I1_001.fastq.gz | head
zless 654_S1_L008_R1_001.fastq.gz | head
zless 654_S1_L008_R2_001.fastq.gz | head

cd ../../..
cat samples.txt

ls slurm_output/
cat slurm_output/countArrayJob_6478353_1.err
cat slurm_output/countArrayJob_6478353_1.out

cd 654/
cd outs/
ls -lah

ls -lah raw_gene_bc_matrices/mm10/
ls -lah filtered_gene_bc_matrices/mm10/

head raw_gene_bc_matrices/mm10/barcodes.tsv
head raw_gene_bc_matrices/mm10/genes.tsv
head raw_gene_bc_matrices/mm10/matrix.mtx
tail  raw_gene_bc_matrices/mm10/matrix.mtx
head filtered_gene_bc_matrices/mm10/matrix.mtx
tail  filtered_gene_bc_matrices/mm10/matrix.mtx