gravatar for dare_devil

2 hours ago by


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

Source link