STAR alignment command.

Question

[amitunited0532]

Which file used as STAR index file? I have downloaded STAR index file from online. Please help me to resolve this problem.

Desktop/STARindex$ STAR --genomeDir /home/amit/Desktop/STARindex --readFilesIn '/media/amit/New Volume/database/SRR1931816.fastq' 
Jun 25 12:54:36 ..... started STAR run
Jun 25 12:54:36 ..... loading genome

EXITING because of FATAL ERROR: could not open genome file /home/amit/Desktop/STARindex/Genome

SOLUTION: check that the path to genome files, specified in --genomeDir is correct and the files are present, and have user read permissions

Jun 25 12:54:36 ...... FATAL ERROR, exiting

[WouterDeCoster]

Do yourself and all of us a favor and first spend some time getting comfortable working with linux and the command line. A starting point could be this tutorial from codecademy, but there are many more available online if you just google. Spending a couple of days on this now will definitely pay of in the future.

[grant.hovhannisyan]

Have you checked this "check that the path to genome files, specified in --genomeDir is correct and the files are present, and have user read permissions"?

[amitunited0532]

How can enable have user read permissions??

[Benn]

type ls -l /home/amit/Desktop/STARindex to see which privileges are present for the files, with chmod command you can change the privileges.

[WouterDeCoster]

/media/amit/New Volume/database/SRR1931816.fastq

Probably not related to your issue but spaces in paths are generally a bad idea.

[Benn]

On unix (linux) you'll need to escape spaces actually, so even if this is not causing this particular error, it will cause an additional error once the index error is solved.

Solution here for.

/media/amit/New\ Volume/database/SRR1931816.fastq

[amitunited0532]

It showing like this,

prashant@prashant-07:~/Desktop/STARindex$ ls -l /home/amit/Desktop/STARindex
ls: cannot access '/home/amit/Desktop/STARindex': No such file or directory

[Benn]

Looks like the directory is not present. Are you sure you didn't make a typo? It looks like you are in this directory already, just type ls -l

[amitunited0532]

After running "ls -l" command it's showing all file in directory.

[Benn]

I know... The permissions are also shown before the files. Please read more about permissions on unix. This way I cannot help you. Also check if all files are there that the STAR aligner needs. Also check if the directory permissions are accessible to you or to STAR.

Answer 1

[Benn]

In the --genomeDir /home/amit/Desktop/STARindex folder, there needs to be a file called Genome. If it is not present, direct to a folder which contains this file (and the rest of the index files). If not present at all, try to index correctly, see previous post here for instructions. If the files are there but you don't have (read) permissions, change them with chmod command.

[amitunited0532]

Please tell me how to use chmod command? I am not much aware from linux.

Thank you

[Benn]

Try to read about it first. chmod is a basic linux command, learning more about basic functions is in my opinion a good idea. You'll probably have to add 'read' permission, but I don't know what ls -l /home/amit/Desktop/STARindex showed you...

Answer 2

[DareDevil]

if you are sure about path to --genomeDir, I would suggest to add / at the end of path as --genomeDir /home/amit/Desktop/STARindex/