Reference Genome Files (.gtf)

This page includes General Transfer Format (.gtf) or related files which allow one to reproduce the alignment from raw (fastq) sequencing data to a specific version of the genome/transcriptome in RNA-seq analysis. Most individuals wanting to use processed versions of Allen Institute sequencing data (e.g., cell x gene matrices) can safely ignore this page. The top table shows a data type-centric view of these files, while the bottom table shows at project-centric view of the same files. In both tables links are colored in blue for convenience.

In the tables below, 'SSv4' indicates any single cell or single nucleus RNA-sequencing or Patch-Seq data that was processed using the SMARTerV4 method, while '10x' indicates any single cell or single nucleus RNA-sequencing data processed using 10x Genomics single-omics or multiomics methods. All mouse and human single cell or single nucleus RNA-sequencing data was aligned to some version of the GRCm38 and GRCh38 genomics, respectively, although file formats and transcriptomics versions differ between rows. NA in the table means no data has every been generated in the relevant slot, while "in process" means that data has been generated but currently is not included in any Allen Brain Map tools. Finally, data from several projects with data generated prior to 2022 (including Patch-seq data) were originally processed using one transcriptome version and have since been converted into the current version. In this case, refer to the relevant Allen Brain Map or scientific public to determine which genome/transcriptome version was used. Abbreviations: GBM = Ivy Glioblastoma Atlas Project; TBI = Aging, Dementia and Traumatic Brain Injury Study; WHB = Whole human brain atlas included in ABC Atlas (May 2024); CTKE = Cell Type Knowledge Explorer; LGN = Lateral Geniculate Nucleus (part of Comparative LGN project)

Reference files by category and species

Reference files by data set