STAR Aligment
1
0
Entering edit mode
9 weeks ago

Hi everyone, I'm trying create star genom index, but command doesn't work. my command is below. Is anyone knows what's wrong with this command? could you please help me, thats 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

tools star • 323 views
ADD COMMENT
0
Entering edit mode

but command doesn't work

what is the error message ?

ADD REPLY
0
Entering edit mode

-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( > )

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
1
Entering edit mode
9 weeks ago
raphael.B ▴ 200
'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.

ADD COMMENT

Login before adding your answer.

Traffic: 2334 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6