What’s a genome index?

Why make a genome index?

Prerequisites for making a genome index

• A fasta file of your genome
• A gtf file of your genome

  • What if I only have a GFF file? → will still work, just add:

    --sjdbGTFtagExonParentTranscript Parent
    

Command

STAR --runThreadN 8 \\
--runMode genomeGenerate \\
--genomeDir genome-index/ \\
--genomeFastaFiles R64-1-1-full.fa \\
--sjdbGTFfile Saccharomyces_cerevisiae.R64-1-1.111.gtf \\
--genomeSAindexNbases 10

• —runThreadN 8: runs STAR on 8 threads; increase if you memory and cores allow
• —runMode genomeGenerate: tells STAR to generate a genome index
• —genomeDir: where to put the output files
• —genomeFastaFiles: path to your fasta file
• —sjdbGTFfile: “specifies the path to the file with annotated transcripts in the standard GTF format. STAR will extract splice junctions from this file and use them to greatly improve accuracy of the mapping. While this is optional, and STAR can be run without annotations, using annotations is highly recommended whenever they are available.”

Resources

https://github.com/alexdobin/STAR

• STAR manual: https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf

From STAR Manual