Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

hisat2-build index for circRNA-seq #426

Open
fengweimin-maker opened this issue Mar 27, 2024 · 0 comments
Open

hisat2-build index for circRNA-seq #426

fengweimin-maker opened this issue Mar 27, 2024 · 0 comments

Comments

@fengweimin-maker
Copy link

fengweimin-maker commented Mar 27, 2024

Hi,
Thanks for a great tool for making genome indexes. I quantify the circRNA-seq data with CIRIquant, but I do not know which of the following ways to construct the index for the circRNA-seq data.
Way 1: hisat2-build -p 20 hg19.fa hg19

Way 2:
hisat2_extract_splice_sites.py hg19.gtf > hg19.ss
hisat2_extract_exons.py hg19.gtf > hg19.exon
hisat2-build -p 20 --ss hg19.ss --exon hg19.exon hg19.fa hg19

Thank you very much!
Best,
Winnie

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant