CustomGenome for R / Bioconductor

A package to append custom FASTA sequences to your genome and annotation files for downstream mapping.

CustomGenome generates a new Ensembl reference genome sequence and annotation files with custom FASTA sequences (e.g. GFP, Tomato) and produces RNA-seq count matrices with them. Genome reference files are fetched and validated directly from Ensembl, user-sequences are then appended to both, and then the new reference files are written to disk. Downstream analysis is then facilitated via Rsubread function wrappers to index the new reference, align user FASTA sequences to it, and then perform quantification for desired features (e.g. exon, utr, etc.)

Installation

Install the package from Bioconductor or Gitlab, ensuring correct dependencies.

From Bioconductor

BiocManager::install("CustomGenome")

From Bioconda

micromamba install -c bioconda -c conda-forge bioconductor-customgenome

From Gitlab

library(remotes)
remotes::install_github("mtekman/CustomGenome",
                        repos = BiocManager::repositories())

Getting Started

Load the library

library(CustomGenome)

Follow the vignette to learn more about how to get started with this package.