STAR - working with binary files in MacOS

Question

[saraG]

Hy everyone,

I would like to carry out an alternative splicing analysis of RNA-seq sata from rat (rn6). I have been trying to install STAR together with rMATS in MacOS as explained by this tutorial:

http://rnaseq-mats.sourceforge.net/user_guide.htm

However, I have had several problem with the compiler because 'clang' is not supported by openMP. I have tried to install gcc in different ways following various several forum recipes with no luck. I decided to use the 'STAR' pre-compiled MAC executable in Downloads/STAR-master/bin/MacOSX_x86_64.

https://groups.google.com/forum/#!topic/rna-star/spxOom9pcNw

They seem to run nicely. However, I got the following in the terminal: -bash: STAR: command not found I am probably doing something silly like not working in the proper directory (?) but I cannot work out my way out of here, does someone have some experience on using pre-compiled binaries to work with STAR? I would really appreciate some guidance.

Answer 1

[GenoMax]

If you are in the directory with STAR executable then explicitly doing ./STAR in command or adding that directory to your $PATH are possible options. Do export PATH=$PATH:/path_to_dir_STAR_executable.

Great UNIX tutorial worth spending a few hours on.

[saraG]

Hi, Using " ./STAR --runMode genomeGenerate ..." within the bin folder works. I am taking a look on the tutorial and it is very useful. Thank you so much for your help.