Reference Genome Database

Author: SeekGene

Time: 1 min

Words: 158 words

Updated: 2026-05-12

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scMethyl + RNA-seq Reference

Overview

SeekSoul™ Methyl Tools uses a unified reference genome database directory provided through --database_dir. This directory stores all resources required for transcriptome and methylation analysis, including the STAR index, genome FASTA, gene annotation, Bismark genome files, and chromosome size BED files.

Recommended Layout

<database_dir>/
|-- bed/
|   |-- chr_len.bed
|   `-- chr_nochrM.bed
|-- fasta/
|   |-- genome.fa
|   |-- genome.fa.fai
|   `-- Bisulfite_Genome/
|-- genes/
|   `-- genes.gtf
`-- star/

Build Guide

You can build the directory from a FASTA file and a GTF file using STAR, samtools, and bismark_genome_preparation.

The full step-by-step tutorial is available here:

• How to build the reference genome database

Notes

• Make sure chromosome names in genome.fa and genes.gtf are consistent.
• bed/chr_nochrM.bed is strongly recommended because the workflow prefers a chromosome list without mitochondrial contigs.
• When running with Docker or Kubernetes, ensure the database directory is mounted inside the container or pod.