Entering edit mode
4.1 years ago
sallyey2
•
0
Hi guys,
I am working on generating genome index in STAR using gtf and fasta files of the mouse genome (GRCm38).
When I look at STAR manual, I notice that --sjdbOverhang defines the length of the genomic sequence around the annotated junction to be used in constructing the splice junctions database. And I can get sjdbOverhang value from ReadLength -1.
Then, how can I get ReadLength from the two files? Is there any specific command to get the length of the genomic sequence?
Thank you so much for your help.
Sequence Length Distribution From A Fastq File
In other words, simply check the length of the reads in the fastq file. Probably it is even enough to simply look at the first few reads. Overall length should identical if you did not do trimming.
It helps me a lot! Thank you so much!