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Cell Ranger mkref Specifications

Process Details

  • Name: Cell Ranger mkref
  • Process UUID: 12WYEn0saKqPrUli1vgs3vnGusQJda
  • Process Group: SingleCell

Overview

Creates a Cell Ranger reference package for single-cell RNA sequencing transcriptome analysis. This process generates a standardized reference genome package that Cell Ranger uses for read alignment and gene expression quantification. The process intelligently handles different GTF file types, applying specific filtering criteria for GENCODE GTF files to select appropriate gene biotypes and exclude problematic transcripts, while using standard protein-coding filters for other GTF formats.

This process is implemented in Bash, which invokes Cell Ranger command-line tools for GTF filtering and reference package generation.

Key Functionality

  • GTF File Type Detection: Automatically detects whether the input GTF is from GENCODE and applies appropriate filtering strategies
  • Gene Biotype Filtering: For GENCODE GTF files, filters for protein-coding genes, long non-coding RNAs, and immunoglobulin/T-cell receptor genes while excluding readthrough transcripts and pseudoautosomal region duplicates
  • Reference Package Generation: Creates a Cell Ranger-compatible reference package combining the filtered GTF annotations with the genome FASTA file

Input/Output Specification

Inputs

Required Inputs

  • genome

    • Description: Reference genome sequence in FASTA format
    • Format: FASTA

  • gtfFile

    • Description: Gene annotation file containing transcript and gene information
    • Format: GTF

Outputs

  • reference
    • Description: Cell Ranger reference package containing indexed genome and filtered gene annotations
    • Format: REF

Parameters & Settings

These parameters can be adjusted in the Foundry UI when running this process.

  • Optional mkgtf filtering parameters
    • Description: By default for Ensembl and NCBI gtf files --attribute=gene_biotype:protein_coding will be used. For Gencode gtf, a custom script will be used for filtering. If you want to add additional attributes for filtering, you can use this field.
    • Default value: (empty string)

References & Resources

  • Tool Documentation: Cell Ranger Reference
  • Related Papers: Zheng, G.X.Y., Terry, J.M., Belgrader, P. et al. Massively parallel digital transcriptional profiling of single cells. Nat Commun 8, 14049 (2017). https://doi.org/10.1038/ncomms14049