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2 hours ago by

India

I run fastqc on the adapter removed fastq file and gets Sequence length : 20-150. Next I want to create index for reference genome using STAR.

Is it the right way to use read length -1 as value for parameter --sjdbOverhang 149

STAR --runThreadN 20 
--runMode genomeGenerate 
--genomeDir /media/analysis/reference/ 
--genomeFastaFiles /analysis/reference/Homo_sapiens.GRCh38.dna.primary_assembly.fa 
--sjdbGTFfile /media/analysis/reference/Homo_sapiens.GRCh38.99.gtf 
--sjdbOverhang 149



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