RUM is an alignment, junction calling, and feature quantification pipeline specifically designed for Illumina RNA-Seq data.
RUM can also be used effectively for DNA sequencing (e.g. ChIP-Seq) and microarray probe mapping.
RUM also has a strand specific mode.
RUM is highly configurable, however it does not require fussing over options, the defaults generally give good results.
Comparative Analysis of RNA-Seq Alignment Algorithms and the RNA-Seq Unified Mapper (RUM) Gregory R. Grant, Michael H. Farkas, Angel Pizarro, Nicholas Lahens, Jonathan Schug, Brian Brunk, Christian J. Stoeckert Jr, John B. Hogenesch and Eric A. Pierce.
RUM is freely available to academics and non-profit organizations. However since RUM uses BLAT, users from industry must first obtain a licence for BLAT from the Kent Informatics Website.
RUM should work anywhere you have most of the standard Unix command-line tools, Perl, and can get the blat, bowtie and mdust binaries to execute; however we haven't tested it on every platform. Unless you have a relatively small genome, then you'll probably need a 64 bit machine. For the human or mouse genome this will definitely be necessary. For a lane of 20 million 100 bp reads, paired-end, expect to use about 100-200 GB disk space.
You will now need the autodie Perl module. If you are using perl >=
5.10, this should already be installed. If not, you may need to
install it. You should be able to install it very quickly by running:
cpan -i autodie
Log::Log4perl is recommended, but not required. You should be able to install it by running:
cpan -i Log::Log4perl
If you have Log::Log4perl, you will be able to control logging output
by modifying the conf/rum_logging.conf file in the RUM
distribution. See http://mschilli.github.com/log4perl/ for more
information.
You can download a specific version of RUM from the tags page on github: https://github.com/PGFI/rum/tags. The latest production release is always available at https://github.com/PGFI/rum/archive/master.tar.gz. The latest bleeding-edge development code (which may be unstable) is available here: https://github.com/PGFI/rum/archive/develop.tar.gz.
You have a few different options for installing RUM, depending on whether you want it in a system location, in an arbitrary user directory, or in another location where you keep Perl modules.
If you have root priviliges and want to install RUM in a system
location like /usr/local, you can now do so using the standard Perl
module installation process:
perl Makefile.PL
make
make install # (may need sudo)If you would rather install RUM in a user-owned directory, you can
simply untar RUM right in the directory where you to install it, and
then run perl Makefile.PL. For example, if you want to have rum
installed in ~/RUM-Pipeline-2.00_13, assuming you have downloaded
RUM-Pipeline-2.00_13.tar.gz to your current directory, you can
simply do:
tar zxvf RUM-Pipeline-2.00_13.tar.gz
cd RUM-Pipeline-2.00_13
perl Makefile.PL
This will place all the rum executables in RUM-Pipeline-2.00_11/bin.
They will find the RUM libraries they need automatically. You may want
to add the bin directory to your path, so that you can run RUM
simply by typing rum_runner:
export PATH="${PATH}:${RUM_HOME}/bin"
rum_runner ...If you don't add the RUM bin directory to your path, you will need to
specify the path to rum_runner when you run it. For example, if
you're in the root of the RUM installation, you can run:
bin/rum_runner ...If you're in the bin directory, run:
./rum_runner ...If you have an alternate location where you keep Perl modules, you
should be able to install RUM there by passing an
INSTALL_BASE=/some/path option to the perl Makefile.PL step. RUM
should automatically find all of its perl modules if you install it in
this manner. For example:
RUM_HOME=~/rum
perl Makefile.PL INSTALL_BASE=$RUM_HOME
make
make installAs in the previous option, you will either need to run rum_runner
using the full path, or add $RUM_HOME/bin to your $PATH.
Once you install the RUM code, you'll want to use the rum_indexes
program to install one or more indexes. 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-indexesWhen you install an index, all the files for that organism will be
placed in a new directory named after the organism. You will need to
specify the index directory when you run RUM. For example, if you
installed the mm9 index by running rum_indexes --prefix ~/rum-indexes, in order to align some reads using that index, you
would run:
rum_runner align --index ~/rum-indexes/mm9 ...
Note that you will need a lot of available disk space in order to install indexes.
At the moment the following indexes are 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 you require a different organism, instructions are given here to build your own custom indexes. Or write us, we may be able to provide it.
After you've installed RUM and one or more indexes, please run
rum_runner help to see usage information. Please also see the main
user guide for an
explanation of the pipeline and the output files.
rum_runner will attempt to write a FATAL message to the error logs if it encounters an error that it can't handle and needs to exit. However, there are some conditions that cause rum_runner to exit immediately, and the program won't log a message in that case. Running out of memory is one example. So if you have a job that just appeared to stop prematurely without leaving any trace of a reason in the log file, it's likely that it ran out of memory.
If you run a job on a single machine and split it up into multiple chunks, it may be using too much memory or CPU time.
For a human genome, each chunk will use about 6 GB of ram, so in order to run it in 10 chunks on a single machine, you'd need at least 60 GB of ram free to be safe.
You probably don't want to use more chunks than you have cores in your system. For example if you have a dual-core system, running a job with 10 chunks will likely create high contention for CPU resources, making your system seem unresponsive.
So if RUM seems to put too much strain on your system, reducing the number of chunks might help.
If you're on a Sun Grid Engine cluster and you run rum with the
--qsub option, it will do a minimal amount of processing up front
and then submit a job to do most of the work. So with SGE you don't
need to run it in the background.
If you're running it locally, you can use nohup rum_runner ... &. It's also very convenient to run rum_runner from within a GNU
screen session.