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STAR Aligment

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
star
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updated by Ram Ram • written by sehriban.buyukkilic • sehriban.buyukkilic

but command doesn't work

what is the error message ?

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written by Pierre Lindenbaum Pierre Lindenbaum 
-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( > )

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updated by Ram Ram • written by sehriban.buyukkilic • sehriban.buyukkilic

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

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written by sehriban.buyukkilic • 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
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updated by Ram Ram • written by sehriban.buyukkilic • sehriban.buyukkilic

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.

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written by raphael.B • raphael.B

1 answer 

'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.

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written by raphael.B • raphael.B

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