STAR Index error

Question

[Sajaa]

Hello,

I am running my first RNA seq analysis and I am getting suck with my alignment. Looking for some help/guidance.

I am running this code

STAR \
  --runMode genomeGenerate \
  --genomeDir genomeIndex \
  --genomeFastaFiles AtChromosome1.fa \
  --runThreadN 2

and getting this error:

STAR: Bad Option: --runMode. Usage: STAR cmd [options] [-find] file1 ... filen [find expression]    STAR cli=name ...
Use STAR -help and  STAR -xhelp to get a list of valid cmds and options.
Use STAR H=help to get a list of valid archive header formats.
Use STAR diffopts=help to get a list of valid diff options.

My index file, genomeIndex, has nothing in it. And the tutorial I'm following SciencePark says this is what I should be generating:

Apr 29 16:55:14 ..... Started STAR run
Apr 29 16:55:14 ... Starting to generate Genome files
Apr 29 16:55:16 ... starting to sort  Suffix Array. This may take a long time...
Apr 29 16:55:16 ... sorting Suffix Array chunks and saving them to disk...
Apr 29 16:56:13 ... loading chunks from disk, packing SA...
Apr 29 16:56:26 ... writing Suffix Array to disk ...
Apr 29 16:56:27 ... Finished generating suffix array
Apr 29 16:56:27 ... starting to generate Suffix Array index...
Apr 29 16:56:48 ... writing SAindex to disk
Apr 29 16:57:00 ..... Finished successfully

I've looked around at so many websites and guides but nothing gives me a working fix for this. Does anybody have an idea of what I might need to change in my initial STAR command?

[GenoMax]

Are you copy pasting commands on MacOS from web? Perhaps the -- are getting converted to smart hyphens. Make sure you type the hyphens in by hand and see if that fixes the issue (and turn off smartquotes/smarthyphens in your keyboard preference.

Answer 1

[dsull]

You should install STAR, not star.

RNA-seq STAR genome mapping