cellranger mkgtf gencode.v28.basic.annotation.gtf gencode.v28.basic.annotation.filtered.gtf 
--attribute=gene_type:protein_coding  
--attribute=gene_biotype:lincRNA
--attribute=gene_biotype:antisense
--attribute=gene_biotype:IG_LV_gene
--attribute=gene_biotype:IG_V_gene
--attribute=gene_biotype:IG_V_pseudogene
--attribute=gene_biotype:IG_D_gene
--attribute=gene_biotype:IG_J_gene
--attribute=gene_biotype:IG_J_pseudogene
--attribute=gene_biotype:IG_C_gene
--attribute=gene_biotype:IG_C_pseudogene
--attribute=gene_biotype:TR_V_gene
--attribute=gene_biotype:TR_V_pseudogene
--attribute=gene_biotype:TR_D_gene
--attribute=gene_biotype:TR_J_gene
--attribute=gene_biotype:TR_J_pseudogene
--attribute=gene_biotype:TR_C_gene




bsub -o log_step0 -q long -W 4000 -n 2 -R span[hosts=1]  -R rusage[mem=20048] "module load cellranger/3.0.2 && cd /share/data/umw_biocore/genome_data/cellranger/human/hg38_gencode_v28 && cellranger mkref --genome=hg38_gencode_v28 --fasta=hg38.fa --genes=gencode.v28.basic.annotation.filtered.gtf --ref-version=3.0.2"