UMD3.1

Version: 2023-04-26

Category: igenomes

Description

The contents of the annotation directories were downloaded from Ensembl on: July 17, 2015.

Gene annotation files were downloaded from Ensembl release 81. SmallRNA annotation files were downloaded from miRBase release 21.

Usage

To find and load available datasets:

$ module avail
$ module load datasets
$ module load igenomes/UMD3.1/2023-04-26

Environment Variables

Variable Name

Value

UMD31_fasta

/anvil/datasets/igenomes/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa

UMD31_bwa

/anvil/datasets/igenomes/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/

UMD31_bowtie2

/anvil/datasets/igenomes/Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/

UMD31_star

/anvil/datasets/igenomes/Bos_taurus/Ensembl/UMD3.1/Sequence/STARIndex/

UMD31_bismark

/anvil/datasets/igenomes/Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex/

UMD31_gtf

/anvil/datasets/igenomes/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.gtf

UMD31_bed12

/anvil/datasets/igenomes/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.bed

UMD31_readme

/anvil/datasets/igenomes/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt

UMD31_mito_name

MT

UMD3.1_HOME

/anvil/datasets/igenomes/Bos_taurus/Ensembl/UMD3.1

RCAC_UMD3.1_ROOT

/anvil/datasets/igenomes/Bos_taurus/Ensembl/UMD3.1

RCAC_UMD3.1_VERSION

2023-04-26