Question: aligning with STAR
0
gravatar for snp87
4.3 years ago by
snp8750
snp8750 wrote:

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.

rna-seq star • 6.5k views
ADD COMMENTlink modified 4.3 years ago by nwon40 • written 4.3 years ago by snp8750
1
gravatar for erictleung
4.3 years ago by
erictleung90
United States
erictleung90 wrote:

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
ADD COMMENTlink written 4.3 years ago by erictleung90

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.

ADD REPLYlink written 4.3 years ago by snp8750

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.

ADD REPLYlink modified 29 days ago • written 2.4 years ago by e.rempel900

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

ADD REPLYlink written 4 weeks ago by spalmer0

Yes, you are right, I change it.

ADD REPLYlink written 29 days ago by e.rempel900
1
gravatar for nwon
4.3 years ago by
nwon40
New Zealand
nwon40 wrote:

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.

ADD COMMENTlink written 4.3 years ago by nwon40
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