Last updated: 05/26/21

The following M21 and M23 reference files are used as inputs to WARP single-cell pipelines (https://github.com/broadinstitute/warp/), such as Optimus and Smartseq2.

These files were built using BuildIndices Pipeline v0.1.0 at https://github.com/broadinstitute/warp/blob/master/pipelines/skylab/build_indices/BuildIndices.wdl.

To replicate all M21 mouse references, including the "genome_ref_fasta", run the BuildIndices Pipeline using the buildindices_mouse_inputs.json configuration file (gs://gcp-public-data--broad-references/mm10/v0/buildindices_mouse_inputs.json).

To replicate all M23 mouse references, including the "snSS2_genome_fa Mouse", run the BuildIndices Pipeline using the buildindices_mouse_snSS2_inputs.json configuration file (gs://gcp-public-data--broad-references/mm10/v0/buildindices_mouse_snSS2_inputs.json).

Reference name	Location
genome_ref_fasta	gs://gcp-public-data--broad-references/mm10/v0/GRCm38.primary_assembly.genome.fa
rrna_intervals	gs://gcp-public-data--broad-references/mm10/v0/gencode.vM21.primary_assembly.annotation.interval_list
gene_ref_flat	gs://gcp-public-data--broad-references/mm10/v0/gencode.vM21.primary_assembly.annotation.refflat.txt
hisat2_ref_index	gs://gcp-public-data--broad-references/mm10/v0/hisat2_primary_gencode_mouse_vM21.tar.gz
hisat2_ref_trans_index	gs://gcp-public-data--broad-references/mm10/v0/hisat2_from_rsem_star_primary_gencode_mouse_vM21.tar.gz
rsem_ref_index	gs://gcp-public-data--broad-references/mm10/v0/rsem_primary_gencode_mouse_vM21.tar
star_index Mouse v21 gs://gcp-public-data--broad-references/mm10/v0/star/star_2.7.9a_primary_gencode_mouse_vM21.tar
star_index Mouse v23 gs://gcp-public-data--broad-references/mm10/v0/star/star_2.7.9a_primary_gencode_mouse_vM23.tar
snSS2_annotation_gtf_introns Mouse: gs://gcp-public-data--broad-references/mm10/v0/single_nucleus/modified_gencode.vM23.primary_assembly.annotation.gtf
snSS2_genome_fa Mouse gs://gcp-public-data--broad-references/mm10/v0/single_nucleus/modified_mm10.primary_assembly.genome.fa
snSS2_star_index Mouse gs://gcp-public-data--broad-references/mm10/v0/single_nucleus/star/modified_star_2.7.9a_primary_gencode_mouse_vM23.tar
annotation_gtf Mouse v23: gs://gcp-public-data--broad-references/mm10/v0/gencode.vM23.primary_assembly.annotation.gtf
annotation_gtf Mouse v21: gs://gcp-public-data--broad-references/mm10/v0/gencode.vM21.primary_assembly.annotation.gtf

For more information regarding the use of the references, please see the overviews of Optimus (https://broadinstitute.github.io/warp/documentation/Pipelines/Optimus_Pipeline/) and Smartseq2 (https://broadinstitute.github.io/warp/documentation/Pipelines/Smart-seq2_Multi_Sample_Pipeline/)

Star index in gs://gcp-public-data--broad-references/mm10/v0/star is created using annotation file mm10/v0/gencode.vM21.primary_assembly.annotation.gtf

Star index in gs://gcp-public-data--broad-references/hg38/v0/single_nucleus/star/ is created using gs://gcp-public-data--broad-references/mm10/v0/single_nucleus/modified_gencode.vM23.primary_assembly.annotation.gtf