Reference Management¶

The Reference Management module ensures that the pipeline has access to all necessary genomic resources, including FASTA files, gene annotations, and specialized repeat/tRNA databases.

Automated Downloads (Refgenie)¶

For standard genomes like mm10 and mm39, 3t-seq uses Refgenie to automatically fetch high-quality references.

Workflow¶

Initialize: A local Refgenie repository is created in results/references/refgenie/.
Pull: The pipeline pulls the fasta and ensembl_gtf (or gencode_gtf) assets.
Specialized Assets:
- RepeatMasker: Fetched and converted to GTF/BED for TE analysis.
- GtRNAdb: Custom tRNA sequences and annotations are downloaded directly from the GtRNAdb servers.

Manual Overrides¶

If you are working with a custom genome assembly or want to use specific local files, you can override the automated downloads.

Label Requirement

label is required even when overriding paths, and must be one of the supported genomes (mm10, mm39). The pipeline uses it to fetch supporting resources (RepeatMasker, GtRNAdb) that match your assembly.

genome:
  label: "mm10" # Required; must match the assembly of your FASTA/GTF
  fasta_path: "/path/to/my_genome.fa"
  gtf_path: "/path/to/my_annotation.gtf"
  annotation_type: "ensembl" # Must be one of: ensembl, gencode, mgi

Chromosome Subsetting¶

The pipeline can filter your FASTA and GTF files to include only a specific set of chromosomes.

genome:
  selected_chromosomes: ["chr19", "chrX"]

Mostly for Testing

This feature is primarily intended for testing purposes or for focusing on specific small genomic regions. Subsetting the genome can significantly simplify the analysis for debugging but may lead to mapping biases if used in production without caution.

Results¶

Location	Description
`results/references/`	Root directory for all genomic resources.
`results/references/STAR/`	The generated STAR genome index.
`results/references/rmsk/`	RepeatMasker annotations (GTF/BED).
`results/references/gtrnadb/`	tRNA sequences and annotations.