Installing indexes

Installing Indexes

After you've installed RUM, you'll need to either install or create indexes for any organisms that you want to map against.

A RUM index provides several things:

• Bowtie index for the genome
• Bowtie index for the transcriptome
• The full genome as a FASTA file
• Gene annotations
• A configuration file that specifies some additional attributes

Each organism's index will be stored in a separate directory, and you'll want a parent directory to contain all of your indexes. Note that indexes can be rather large -- the latest index for the human genome (hg19) requires about 6.3 GB of disk space.

We currently have the following indexes available:

• Homo sapiens (build hg19) (human)
• Homo sapiens (build hg18) (human)
• Mus musculus (build mm9) (mouse)
• Danio rerio (build danRer7) (zebrafish)
• Drosophila melanogaster (build dm3) (fruit fly)
• Anopheles gambiae (build anoGam1) (mosquito)
• Caenorhabditis elegans (build c36) (nematode worm)
• Saccharomyces cerevisiae (build sacCer3) (yeast)
• Rattus norvegicus (build m4) (rat)
• Sus scrofa (build susScr2) (pig)
• Canis lupus familiaris (build canFam2) (dog)
• Pan troglodytes (build panTro2) (chimpanzee)
• Pongo pygmaeus abelii (build ponAbe2) (orangutan)
• Macaca mulatta (build rheMac2) (rhesus monkey)
• Gallus gallus (build galGal3) (chicken)
• Plasmodium falciparum (build 06-2010) (malaria parasite)
• Arabidopsis thaliana (build TAIR10) (arabadopsis)

If the index you need is not in this list you can either create your own index, or write us and we may be able to help.

You can install an index from the list above using the interactive rum_indexes script, which comes with the RUM installation. By default it will install indexes in the location where you installed RUM itself, but you can use the --prefix option to tell it to install indexes somewhere else:

# Install them where you installed rum
rum_indexes

# Install them in ~/rum-indexes
rum_indexes --prefix ~/rum-indexes

The script will show you the list of indexes and prompt you for the ones to install. You can do some other index maintenance tasks using rum_indexes; please see rum_indexes --help for more information.

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Next: Creating indexes or running RUM