Use of --sjdbOverhang option in STAR program

Question

[Himanshu Bhusan Samal]

Hi .. I am working on Human RNA-Seq data. I want to generate the genome indexes using STAR program. And, I am working on Ensembl GRCh37 file. Can anybody suggest me why I need the --sjdbOverhang option in the genome generation step ..? And, what is the ideal value to set for this parameter ..

thanks and regards, Himanshu Bhusan Samal

Answer 1

[John]

See here: Sjdboverhang Option In Star

Also that is the first hit if you Google "sjdbOverhang" :P

EDIT: Actually, the entire first page from the Google results is people asking what is sjdbOverhang and why do they need it. If it's value should be the readlength -1, why is it even a parameter? The number of collective human hours wasted on trying to figure out what sjdbOverhang is, what it's value should be, manually determining read lengths for every FASTA file used, and then typing that in to the command line -1; it makes me feel... slightly depressed.

[Himanshu Bhusan Samal]

Thank you so much and I am trying to finalize it.