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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
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
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