Hello everyone!
I have interesting question asked by my professor and I could not find relevant answer anywhere.
Why are we seeing up and down pattern on transcript abundance? Example RNA seq data for a gene from a rice transcriptome data base is attached. LOCUS ID is highlighted in yellow and transcript abundance is in below three samples after drought treatment.
The question is ,why the signal level is not uniform on Exons? is it low signal reads? Why there are gaps or sudden fall in signals? ( which are Marked in Red arrows) How to read and understand this? and I know this is the common pattern in RNA-seq data, but I don’t know why? It’s an interesting question asked by my professor! can any bioinformatician help me understand this? Thanks in advance.
I am not an expert in this by any means, but I have read a lot and have seen this type of data and interpreted it before as well. I can give you what I know from my experience and others may chime in.
It is a read out of transcripts that correspond to that particular site. it might be referred to as base resolution expression of the particular sequence. Essentially the higher number of transcripts that coincide with that particular sequence the higher the score. It could be areas that were difficult to resolve due to all kinds of aspects. 1) Sequence has a lot of repeats if that was the case you would see the same resolution in the other two samples but that does not seem to be the case. These areas might be resolved better if you increase the read depth of the study.
2) It may be more suggestive of a difficulty to read them. These results may be affected by post modification of the RNA as well.
This paper describes this is clinical samples but that does not restrict the affect only to humans post-modification
Sci Adv. 2021 Aug; 7(32): eabd2605.
Published online 2021 Aug 4. doi: 10.1126/sciadv.abd2605
PMCID: PMC8336963
PMID: 34348892
Judging by the fact the title on the samples say drought I might think a more epigenetic effect (Post-modification of the RNA maybe due to stress)
Thanks for the informative response and the link John Powers . As you mentioned, there may be lot of factors involved in it, especially the difficult sequences that might resulted in poor reads (I assume) and high likely the post modifications of RNA due to epigenetic modifications. I need to read more to understand this. Thanks again.
Hi,
The answer given by John Powers is correct. These reflects number of aligned reads from several RNA seq experiments. And it is true that the read frequency is not going to be same due to multiple reasons some of which are mentioned above.
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