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bioinfo-biols / CIRIquant

circular RNA quantification tools
https://sourceforge.net/projects/ciri/files/CIRIquant
MIT License
27 stars 17 forks source link

hisat2-build index for circRNA-seq #65

Open fengweimin-maker opened 3 months ago

fengweimin-maker commented 3 months ago

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

Kevinzjy commented 3 months ago

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.

fengweimin-maker commented 3 months ago

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! image

fengweimin-maker commented 3 months ago

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! image

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

best, Winnie