#@ COUNT / include_intron (default) homd=/home/tom/.cellranger mus=$homd/refdata-gex-mm10-2020-A hs=$homd/refdata-gex-GRCh38-2020-A dir_in=AGED dir_out=MAP prefix=Aged cpu=10 memory=128 cellranger count \ --id=$dir_out \ --fastqs=$dir_in \ --sample=$prefix \ --transcriptome=$mus \ --localcores=$cpu \ --localmem=$memory #@ custom reference # Get GTF/GENOME from ENSEMBL and uncompress # Filter GTF cellranger mkgtf \ a.gtf \ out.gtf \ --attribute=gene_biotype:protein_coding # Make Ref cellranger mkref \ --genome=outdir \ --fasta=g.fa \ --genes=out.gtf