What should be the value of Sjdboverhang in STAR?

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

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written 5.4 years ago by DareDevil

Why do you doubt your choice? Have you read other posts, such as this one?

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written 5.4 years ago by Friederike

0 answers

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