STAR alignment command.

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


RNA-Seq


alignment


sequence


assembly


rna-seq

• 5.2k views

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.

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


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