single exon quantification using RNA-seq

Question

[Qianjiang(QJ) Hu]

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.

[ATpoint]

Before doing non-standard things I would make a browser track (bedGraph/bigwig) file using bedtools genomecov or deeptools bamCoverage and look at the in control vs KO in the Integrated Genome Browser. That might give an idea what to check next. Look at exon coverage of all isoforms, so basically loading a GTF reference file (for example GENCODE) and right-click it to expanded view, to see all isoforms. Check how reads are distributed. Maybe other isoforms exist, maybe they're now preferred in that particular model, who knows.

[Qianjiang(QJ) Hu]

Thank you!