===
EF2
===

Version: 2023-04-26

Category: **igenomes**

Description
-----------

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

Annotation files in this directory and subdirectories were downloaded from EnsemblGenomes release 27. Ensembl now uses the name 'ASM294v2, May 2009' for this assembly.

Usage
-----

To find and load available datasets::

    $ module avail
    $ module load datasets
    $ module load igenomes/EF2/2023-04-26
Environment Variables
-------------------

.. list-table::
   :header-rows: 1
   :widths: 25 75

   * - **Variable Name**
     - **Value**
   * - ``EF2_fasta``
     - ``/anvil/datasets/igenomes/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa``
   * - ``EF2_bwa``
     - ``/anvil/datasets/igenomes/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/version0.6.0/``
   * - ``EF2_bowtie2``
     - ``/anvil/datasets/igenomes/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/``
   * - ``EF2_star``
     - ``/anvil/datasets/igenomes/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/STARIndex/``
   * - ``EF2_bismark``
     - ``/anvil/datasets/igenomes/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex/``
   * - ``EF2_gtf``
     - ``/anvil/datasets/igenomes/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.gtf``
   * - ``EF2_bed12``
     - ``/anvil/datasets/igenomes/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.bed``
   * - ``EF2_readme``
     - ``/anvil/datasets/igenomes/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt``
   * - ``EF2_mito_name``
     - ``MT``
   * - ``EF2_macs_gsize``
     - ``1.21e7``
   * - ``EF2_HOME``
     - ``/anvil/datasets/igenomes/Schizosaccharomyces_pombe/Ensembl/EF2``
   * - ``RCAC_EF2_ROOT``
     - ``/anvil/datasets/igenomes/Schizosaccharomyces_pombe/Ensembl/EF2``
   * - ``RCAC_EF2_VERSION``
     - ``2023-04-26``