STAR 2.5

Spliced Transcripts Alignment to a Reference © Alexander Dobin, 2009-2015

AUTHOR/SUPPORT

Alex Dobin, dobin@cshl.edu https://groups.google.com/d/forum/rna-star

MANUAL

https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf

RELEASEnotes contains detailed information about the latest major release

DIRECTORY CONTENTS

• source: all source files required for compilation
• bin: pre-compiled executables for Linux and Mac OS X
• doc: documentation
• extras: miscellaneous files and scripts
• STAR-Fusion: fusion detection developed by Brian Haas, see https://github.com/STAR-Fusion/STAR-Fusion for details. To populate this submodule, clone STAR with git clone --recursive https://github.com/alexdobin/STAR
• STAR-Fusion-x.x.x: latest release of the STAR-Fusion

COMPILING FROM SOURCE

To compile STAR from source, you must first download the latest release and uncompress it and then build it.

NOTE: The following instructions only work when obtaining the source using git. At least until a new version is released which incorporates the top-level Makefile.

Linux

# Get latest STAR source from releases
wget https://github.com/alexdobin/STAR/archive/STAR_2.5.2a.tar.gz
tar -xzf STAR_2.5.2a.tar.gz
cd STAR_2.5.2a

# Alternatively, get STAR source using git
git clone https://github.com/alexdobin/STAR.git
cd STAR

# Build STAR
make STAR

# To include STAR-Fusion
git submodule update --init --recursive

# If you have a TeX environment, you may like to build the documentation
make manual

Mac OS X

# Get latest STAR source from releases
wget https://github.com/alexdobin/STAR/archive/STAR_2.4.2a.tar.gz
tar -xzf STAR_2.4.2a.tar.gz
cd STAR_2.4.2a

# Alternatively, get STAR source using git
git clone https://github.com/alexdobin/STAR.git
cd STAR

# To include STAR-Fusion
git submodule update --init --recursive

# Build STAR
cd source
make STARforMacStatic

If g++ compiler (true g++, not Clang sym-link) is not on the path, you will need to tell make where to find it:

# Build STAR
cd source
make STARforMacStatic CXX=/path/to/gcc

Developers

STAR developers with write access to https://github.com/alexdobin/STAR can update the STAR-Fusion submodule to a specific tag by following these steps:

git clone --recursive https://github.com/alexdobin/STAR.git
cd STAR
# or:
#
# git clone //github.com/alexdobin/STAR.git
# cd STAR
# git git submodule update --init --recursive

# checkout a specific tag for the submodule
cd STAR-Fusion
git checkout v0.3.1

# Commit the change
cd ../
git add STAR-Fusion
git commit -m "Updated STAR-Fusion to v0.3.1"

# Push the change to GitHub
git push

HARDWARE/SOFTWARE REQUIREMENTS

• x86-64 compatible processors
• 64 bit Linux or Mac OS X
• 30GB of RAM for human genome

LIMITATIONS

This release was tested with the default parameters for human and mouse genomes. Please contact the author for a list of recommended parameters for much larger or much smaller genomes.