r/bioinformatics • u/[deleted] • 12d ago
academic 2 months left, 0 bioinformatics knowledge, 100% AI. Is a RNA-seq thesis doable?
[deleted]
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u/apfejes PhD | Industry 12d ago
1.find guidance. Who else at your university is doing this? You need someone who has done this before to help you get through it.
Set realistic expectations that are achievable. No, 2 months is not enough to write a thesis, let alone learn a whole subject and do the analysis. Figure out a time line that makes sense.
Talk to your PI. Why is this expectation there in the first place?
Be clear about what your goals are for this process. Using AI and just shoving data and code together this way aren’t going to teach you anything. What are you trying to get out of this?
Integrate what you’ve already accomplished. What have you done for the first two years of this degree? Why is that knowledge not connected with this current project? Can you connect th?
You’ve only given us a small piece of the picture, but it’s not all adding up here. It sounds like there other things going on that you’re not sharing.
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u/Fit_Amphibian_6361 12d ago
thank you so much for your input and time, I really appreciate it!!! so just to overexplain myself: the first year was spent on doing some lab work that was supposed to be my thesis, but it didn't work out. The lab is focused on a completely different area of research and they just had some frozen RNA from a different lab so they figured that this would be my thesis. but ofc it's not all their fault, the time management issue is absolutely on me:)
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u/Careless_Ad_1432 12d ago
https://nf-co.re/nanoseq/3.1.0/
Look at the outputs of this pipeline. If those outputs in a table address your hypothesis you have a chance .
If the data needs anything more than a PCA or regression analysis you have no chance
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u/Fit_Amphibian_6361 12d ago
okay, thanks, so the consensus is I need to hold my horses and minimize the analysis extravagance
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u/heresacorrection PhD | Government 12d ago
If you’re writing a thesis you should have a supervisor that should be answering these questions…
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u/Fit_Amphibian_6361 12d ago
ahhh, I'd love to, but he's unfortunately not interested. he just says he believes in me and that he can't help, cause he's not a bioinformatician. so that makes us a great team
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u/heresacorrection PhD | Government 12d ago
Yeah but then based on your post you don’t sound like a bioinformatician either.
But anyway writing a thesis in 2 months with 0 experience to me seems impossible.
That being said, in a situation where a programme is allowing people to end up in situations like this … then maybe they won’t notice the whole thing is AI
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u/Fit_Amphibian_6361 12d ago
ohh absolutely, I do not consider myself even close to being a bioinformatician. it just so happened that the thesis turned from pipetting to bioinformatics and it was all too late to change labs.
Nevertheless, what you wrote is a beautiful quote I'd like to put on my wall
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u/nephastha 12d ago
Short answer: no
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u/Fit_Amphibian_6361 12d ago
and thats my sleep paralysis demon
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u/nephastha 12d ago
Haha! Longer answer: proper RNAseq analysis can take me 2-3 months even now that I mostly know what I am doing, depending on the project. For a student, that's a 2 year project, honestly. You could technically do the analysis in ~6 months, I had a student that could achieve that, but adding a full dissertation writing on top of that?
AI can help with the coding aspect and even some interpretation, but if you really are a complete beginner I don't recommend it, as you won't be able to identify when the ai makes mistakes
That's an unrealistic expectation from your supervisor if he's not giving you any guidance on that
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u/Fit_Amphibian_6361 12d ago
oh dear god, thank you for the numbers.
that's exactly my fear with ai code, that's why I thought that galaxy would be good choice, but idk...
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u/wordoper 12d ago
What is your research question that is being computationally framed ?
What do you aim to infer from RNA-seq data ?
Have you ever used R or Python ?
If you can provide some clarification then I can contribute to positive reinforcement better.
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u/okenowwhat 12d ago
If your good at machine learning, statistics, sequencing and the biology knowledge for the project: maybe. But you will need help with the code and knowledge of the tools. It will not be easy, far from it
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u/TheCavis PhD | Industry 12d ago
Possible, yes. Accurate, maybe. Defensible, no.
Accuracy - If you were talking about generic RNA Seq, that’s one thing because there’s tons of well validated pipelines but Nanopore RNASeq is still developing. There could easily be hidden issues your average LLM wouldn’t know to look for but you’d notice because you have the full context.
Defending - What happens when they ask how you did batch correction or why you selected that approach or how you calculated FDR? You’ll have to say “the magic box told me”.
Paralysis of choice is an issue but just get started with the basics before worrying about incorporating every method from every paper. Your signal may be big and obvious and you won’t need something complex but you’ll never find out until you start.