I am pretty new to this field and I require some help with analysis of some RNA-Seq data that I have. I have two different samples. In sample 1, we have done some modifications so that the NMD machinery will not work properly in it. So, the ultimate task is to prove that NMD machinery will not work well in sample 1 when compared to sample 2. For that, we compare the levels of transcripts with premature termination codons in both. Sample 1 should have a higher number of them, because the NMD is compromised, so these abnormal transcripts (ones with premature termination codon) will be seen in higher level. Wheras in sample 2, NMD is functional. It degrades most of these these abnormal transcripts.
Now, I have RNA-Seq data of both these samples. From this, I want to compare the expression of those transcripts with premature termination codon, in both the samples. I would also appreciate recommendations for tools to use for this. Thanks in advance.
Side note: It's not "RNA Seq", they're not 2 separate words. I've seen RNAseq and RNA-seq used interchangeably, but never RNA Seq.