Entering edit mode
3.7 years ago
DareDevil
★
4.3k
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
Why do you doubt your choice? Have you read other posts, such as this one?