Question: What files and filtering criteria were used for generating 10x references?
Answer: Pre-built single-cell gene expression analysis reference packages for human and mouse genomes are available on the 10x support site. The files and filtering criteria used for creating these reference packages are described below.
However, users can also create custom reference packages for other species by using the instructions here. The FASTA and GTF files may be downloaded directly from Ensembl.
Human:
GRCh38
The following criteria were used for filtering this GTF:
cellranger mkgtf Homo_sapiens.GRCh38.84.gtf Homo_sapiens.GRCh38.84.filtered.gtf \
--attribute=gene_biotype: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
hg19
The following criteria were used for filtering the GTF:
cellranger mkgtf Homo_sapiens.GRCh37.82.gtf Homo_sapiens.GRCh37.82.filtered.gtf \
--attribute=gene_biotype:protein_coding \
--attribute=gene_biotype:lincRNA \
--attribute=gene_biotype:antisense
Mouse:
mm10
The following criteria were used for filtering the GTF:
cellranger mkgtf Mus_musculus.GRCm38.84.gtf Mus_musculus.GRCm38.84.filtered.gtf \
--attribute=gene_biotype:protein_coding \
--attribute=gene_biotype:lincRNA \
--attribute=gene_biotype:antisense