Description of parameters:
--runMode
genomeGenerate
--runThreadN
Number of Threads
--genomeDir
/path/to/genomeDir
--genomeFastaFiles
/path/to/genome/fasta1 /path/to/genome/fasta2 ...
--sjdbGTFfile
/path/to/annotations.gtf
--sjdbOverhang
Read Length -1
For a more detailed explanation of the different options of STAR to build a Genome
Index read the STAR Manual on GitHub:
https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf, or type
in the terminal. After generating the Genome Index some more files with information about
exonic gene sizes or chromosome sizes can be created using Bioconductor packages in R or
the command line tool.
The detailed process on how to create these additional files is depicted below.
Create exonic gene sizes in R [2]
Extract geneID and gene symbol and gene_type from gtf annotation file
8 Reference Genome
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