aligning with STAR

Question

[snp87]

Hi, I am trying to align some RNAseq data using STAR. I am new to analysing RNAseq data and know only basic scripting. I'm having a bit of trouble installing (and understanding the installation instructions) STAR on a Mac OS X platform. Are there specific instructions (scripts) anyone could point me to? Any help will be much appreciated.

Answer 1

[nwon]

Once you have downloaded and unzipped the package. There is already a precompiled executable which can be found in:

STAR-master/bin/MacOSX_x86_64

So, either explicitly state the path to the executable or export the path (if you are using bash in MacOSX):

export PATH=$PATH:/path/to/STAR-master/bin/MacOSX_x86_64

That should work.

Answer 2

[erictleung]

An easy way to install STAR would be to use Homebrew, in case you don't already have it. It not only have Unix utilities you can download but there a plethora of science tools also available. Once you have Homebrew installed, installing STAR can be as easy as

brew install homebrew/science/rna-star

I hope that proves to lower the barrier to at least playing around with STAR.

Otherwise, I feel that their instructions were pretty clear.

# 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

# Build STAR
cd source
make STARforMacStatic

[snp87]

Thanks so much for the information about homebrew - that's very helpful to know. I was having trouble with the 'make' command at the end so decided to go with homebrew to download STAR.

[e.rempel]

After depreciation of homebrew/science you have to use

brew tap brewsci/science
brew install rna-star

As of now (21.09.2020), version 2.5.3a will be installed.

[spalmer]

I think there's a typo there: tab should be tap

[e.rempel]

Yes, you are right, I change it.