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Hisat2 index with splice sites

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  • Hisat2 index with splice sites

    Hello,

    I would like to detect lncRNAs from RNA-seq data. Initially, I'm using Hisat2 for aligning the samples. For this I downloaded the human genome hisat2 index "genome_snp_tran" from the hisat2 webiste. [https://ccb.jhu.edu/software/hisat2/manual.shtml]

    I would like to know whether this "genome_snp_tran" is built with splice sites already?

    Why splice sites are needed? If there are necessary and if the genome index I downloaded is not built with splice sites how can I get the splice sites?

    thankyou
    bvk
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