What should be the value of Sjdboverhang in STAR?
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6 months ago
dare_devil ★ 1.4k

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
STAR index reference sjdbOverhang • 238 views
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