Single-Cell-RNA-seq-Benchmark

cellranger count --id=run_count_3kpbmc --fastqs=~/pmbc/pbmc3k_fastqs --transcriptome=/home/jzhou417/cellranger/refdata-cellranger-GRCh38-3.0.0 --expect-cells=3000 --indice=SI-NA-E12

cellranger mat2csv run_c

cellranger mat2csv filtered_feature_bc_matrix pbmc3k.csv

For seqtk

1. Install

git clone https://github.com/lh3/seqtk.git; cd seqtk; make

seqtk.sh

For cellranger

cellranger count --id run_count_3kpbmc_70 --fastq=/nethome/jzhou417/all_pbmc3k/70/0.7 --transcriptome=/nethome/jzhou417/cellranger/refdata-cellranger-GRCh38-3.0.0 --expect-cells=3000 --indices=SI-NA-E12