STAR Aligment

Question

[sehriban.buyukkilic]

Hi everyone, I'm trying create star genom index, but command doesn't work. my command is below. Does anyone know what's wrong with this command? Could you please help me, thanks a lot

'STAR \
  --runThreadN 2 \
  --runMode genomeGenerate \
  --genomeDir /truba/home/sbuyukkilic/rnaseq//genomeDir \
  --genomeFastaFiles /truba/home/sbuyukkilic/rnaseq/files/GRCh38.primary_assembly.genome.fa \
  --sjdbGTFfile /truba/home/sbuyukkilic/rnaseq/files/gencode.v42.annotation.gtf \
  --sjdbOverhang 50

[Pierre Lindenbaum]

but command doesn't work

what is the error message ?

[sehriban.buyukkilic]

-bash-4.2$ 'STAR --runThreadN 2 --runMode genomeGenerate --genomeDir /truba/home/sbuyukkilic/rnaseq//genomeDir --genomeFastaFiles /truba/home/sbuyukkilic/rnaseq/files/GRCh38.primary_assembly.genome.fa --sjdbGTFfile /truba/home/sbuyukkilic/rnaseq/files/gencode.v42.annotation.gtf --sjdbOverhang 50
>

This is only on screen, there is nothing beside this( > )

[sehriban.buyukkilic]

ı check it out, that means there is missing something on command. But what?

[sehriban.buyukkilic]

I did in different way, but there is another error.

-bash-4.2$ ./STAR --runThreadN 2 --runMode genomeGenerate --genomeDir /truba/home/sbuyukkilic/rnaseq//genomeDir --genomeFastaFiles /truba/home/sbuyukkilic/rnaseq/files/GRCh38.primary_assembly.genome.fa --sjdbGTFfile /truba/home/sbuyukkilic/rnaseq/files/gencode.v42.annotation.gtf --sjdbOverhang 50
-bash: ./STAR: cannot execute binary file

[raphael.B]

this is not a STAR error. It is a bash issue. You are trying to execute the './STAR', but it is a binary file, not a bash file.

Answer 1

[raphael.B]

'STAR --runThreadN 2 --runMode genomeGenerate --genomeDir /truba/home/sbuyukkilic/rnaseq//genomeDir --genomeFastaFiles /truba/home/sbuyukkilic/rnaseq/files/GRCh38.primary_assembly.genome.fa --sjdbGTFfile /truba/home/sbuyukkilic/rnaseq/files/gencode.v42.annotation.gtf --sjdbOverhang 50

I think the initial ' is the problem here. You are starting a text block, but not closing it.