single exon quantification using RNA-seq

single exon quantification using RNA-seq

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Hi, I have done the RNA-seq (mRNA) on gene knockout mice. I have evaluated the gene knockout from protein level. However, after RNA-seq data analysis, I didn’t see down-regulation of this gene. I used the pipeline Hisat2-HTseq to do the RNA-seq analysis. Technicholy, this gene knockout has exons 6-7 deleted from genes. So, I am wondering whether there are ways to only quantify exons 6-7 of this gene from RNA-seq data.


mRNA


RNA-seq

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