Originally posted by Nino
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This is done with the following command:
STAR --runMode genomeGenerate --genomeDir /path/to/GenomeDir --genomeFastaFiles /path/to/genome/fasta1 /path/to/genome/fasta2 --runThreadN <Nthreads>
If you want to use annotations for improved mapping accuracy, you also need to use:
--sjdbGTFfile /path/to/Annot.gtf --sjdbOverhang <N>, where ideally N=ReadMateLength-1, or you could generically use ~100.
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