Create iGenome : This script creates an iGenome « LIKE » reference genome.  The iGenomes Illumina's bundled referece and annotation packages to be used with GenomeStudio.  an iGenome has the following simplified directory tree structure :
Mus_musculus/         	     	     		       	 	## Organisms/species
└── Ensembl							## Format/Data source
    ├── Grcm38							## Reference Genome release
    │   ├── Annotation						## Feature annotation file
    │   │   ├── Genes
    │   │   │   └── genes.gtf, refFlat.txt, refGene.txt		## gene annotation files
    │   │   ├── SmallRNA
    │   │   │   └── mature.fa precursor.fa			## Fasta files from miRBase
    │   │   └── Variation
    │   │       └── Mus_musculus.gvf				## Genomic variation
    │   └── Sequence
    │       ├── AbundantSequences				## fasta files
    │       │   └── adapter_contam1.fa* MT.fa* musRibosomal.fa*
    |	    |	    phix.fa* polyA.fa* polyC.fa*		## * refers to .fa.2bpb and .fa.vld index
    │       ├── Bowtie2Index
    │       │   └── genome.*.bt2 genome.fa -> ../path/to/ref	## Bowtie2 indexes and link to genome.fa
    │       ├── BowtieIndex
    │       │   └── genome.*.ebwt genome.fa -> ../path/to/ref	## Bowtie1 indexes and link to genome.fa
    │       ├── BWAIndex
    │       │   └── genome.fa.* genome.fa -> ../path/to/ref	## BWA indexes and link to genome.fa
    │       ├── Chromosomes
    │       │   └── 1.fa ... 19.fa X.fa Y.fa MT.fa		## Fasta files from individual chromosomes
    │       ├── Squashed-Mus_musculus-Ensembl-Grcm38
    └──     └── WholeGenomeFasta
        	└── genome.fa genome.fa.fai genome.dict		## Genome Reference in Fasta, samtools faidx
		    	      		    			## and picard CreateGenomeDictionary.jar index
								## files
The directory structured is simplified as in addition to Annotation and Sequence, directories, there is an additional GenomeStudio which contains symbolic to the appropriate locations, and each directory has an Archives or versionXX directory where the data is contained and then sym-linked to the files shown here.  The symbolic link strategy was not reconstructed, however, the essence of the data structure was preserved in this script shuch that it resembles the above.
The location and additional README files will be downloaded along with the data for reference.
Sort iGenome:  Should you have an exisiting copy of an iGenome, you can change the order by which chromosomes are sorted using this script.  The script goes into WholeGenomeFasta/ and reconstructs the reference genome.fa in a more human like order i.g. 1..19, MT, X and Y (uses sort -V).  It uses the same order for the annotation files.  The script also re-generates the indexes where necesary for consistancy.
Initial commit
Added description of repository
Debugging WholeGenomeFasta/ cleanup
adding to README.md
Added code for downloading ensGene.txt.gz, and convert gtf to refFlat format.
Merge branch 'master' of https://github.com/RodrigoGM/mouseomics

Conflicts: create.igenome.sh; Resolved