For RNAseq analysis, you will need several files that correspond to your reference genome of interest. These files can be found at:

http://support.illumina.com/sequencing/sequencing_software/igenome.html.

Select your genome of interest (ex: UCSC mm9). This will download a compressed .tar.gz folder that you will need to extract. This will take 2 extraction steps on a Windows machine or 1 step on a Mac or Unix OS. This folder is fairly large and may occupy about 40 GB of storage space after extraction. The following .txt file describes the directory structure of the iGenomes folder.

iGenomes_Overview.txt

You will need a reference genome fasta file (genome.fa) and corresponding fasta index file (genome.fa.fai), a transcriptome file (genes.gtf), and the index files for either Bowtie (*.ebwt), Bowtie2 (*.bt2), or HISAT2 (*.ht2). As of this writing (July 13, 2016), the HISAT2 index files are not located on the iGenomes website and must be downloaded from:

https://ccb.jhu.edu/software/hisat2/index.shtml.

For simplicity, the genome files for the mouse genome (either UCSC mm9 or mm10) can be found on the CMRG Cloud at:

/Buchholz_Kyle/CMRG_Checkout/Genome_Files

To utilize these files, simply copy the either folder for the genome of interest (either mm9 or mm10) to your desired location. If working on the NBCR rocce cluster, you will want to copy these to your /data/scratch/<username>/ folder.