README.md

In Oumaimalh/BSgenome.oryza: Chromosome plus MT plus rDNA sequences for riz (based on ensembl)

BSgenome.oryza

Intrduction

An infrastructure package Bsgenome is available for acccesing,analyzing,creating or modifying Biostrings-based genome data package.And the main goal of this document is to explain the steps in building the Bsgenome rice package.

Step1: Install the BSgenome package

```{r eval=FALSE} if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("BSgenome", version = "3.8")

# Step2: Download the genome sequence

Download the fasta files for the desired genome sequence.In our case the oryza_sativa had 12 Chromosones downloaded separately.
Those fasta files were found in this [repository](ftp://ftp.ensemblgenomes.org/pub/release-46/plants/fasta/oryza_sativa/dna/).

# Step3: Prepared my files

I created a new folder on my Desktop and set this as my working directory:

```{r eval=FALSE}
setwd("/Users/asus/Desktop/Atelier1/Bsatelier")

• Create my seqs_srcdir file :
• In this file i put all the Downloaded fasta files and named them starting with Chr so it can be more readable.
• Create my Seed file
• The seed file contains all the relevant metadata for the BSgenome package

```{r eval=FALSE} Package: BSgenome.oryza Title: Full genome sequence for Vibrio cholerae O1 biovar El Tor str N16961 Description: Oryza sativa full genome as provided by MSU (MSU7 Genome Release) and stored in Biostrings objects. Version: 1.0.0 Author: Oumaima lahiani organism: Oryza sativa common_name: Rice provider: MSU provider_version: MSU7 release_date: 2020/05 release_name: MSU7 Genome Release source_url: ftp://ftp.ensemblgenomes.org/pub/release-46/plants/fasta/oryza_sativa/dna/ organism_biocview: oryza BSgenomeObjname: oryza seqfiles_suffix: .fa seqs_srcdir:/Users/asus/Desktop/Atelier1/Bsatelier/inst/extdata seqnames: c('chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12')

* The two important notes that crossed my path were:
  + The BSgenomeObjname is important because this is the name you will use to access the package in R once it has been installed.

  + For genomes with multiple chromosomes, list them as a vector.

# step4: Forge the package
* The package is forged using the forgeBSgenomeDataPkg function.

* Simply use the name of the seed file as the only argument and it will create your package files to the same directory.

```{r eval=FALSE}
forgeBSgenomeDataPkg("/Users/asus/Desktop/Atelier1/Bsatelier/DESCRIPTION")

Note: To run the function again, delete the previous package files first.

step5: Installing my genome package

To install the genome package you will need to use the Mac command line (Terminal). 1. Close R 2. Open Terminal 3. In the Terminal i needed to navigate to my working directory:(using cd) 4. ```{r eval=FALSE} Run R CMD build BSgenome.oryza to compile the package Run R CMD check BSgenome.oryza.tar.gz to check it Run R CMD INSTALL BSgenome.oryza_1.0.0.tar.gz

# step6: Loading and accessing the genome in R
To use the genome in R you will need to load the package using the library() function.

```{r eval=FALSE}
library(BSgenome.oryza)

Documentation

• How to forge a BSgenome data package
• BSgenome.Osativa.MSU.MSU7
• build_custom_BSgenome_TxDb

Oumaimalh/BSgenome.oryza documentation built on May 18, 2020, 12:02 a.m.