hisat2-build index for circRNA-seq

Question

hisat2-build index for circRNA-seq

Opened this issue a year ago · 3 comments

Hi,
Thanks for a great tool for the analysis of circRNA-seq. 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

Answer 1 · 2024-03-27T11:25:19.000Z

Hi @fengweimin-maker, both ways work, but I would recommend you to use the 2nd way because it can improve the accuracy of aligning the splice site.

Answer 2 · 2024-03-30T13:33:49.000Z

Hi@Kevinzjy,
Thank you very much for reply so quickly!
But I have another question: Why is the out file in the 'gene' directory empty? If I miss this file, I can't get the gene count matrix.
Thank for your reply again!

Answer 3 · 2024-03-31T08:54:11.000Z

Hi@Kevinzjy, Thank you very much for reply so quickly! But I have another question: Why is the out file in the 'gene' directory empty? If I miss this file, I can't get the gene count matrix. Thank for your reply again!

Hi@Kevinzjy,
I have solved this problem, it is the gtf version of the problem. Thanks again for such a good software.

best,
Winnie