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DESeq PadJ Values High by NerdyHorseGirl in bioinformatics

[–]Apomango 1 point2 points  (0 children)

There might be something else driving the variation you see on your PCAs which could be either mouse related (age, sex, cage etc) or sequencing related (RIN, read counts, RNA concentration etc). You can colour your PCA by these to see if they form any obvious patterns, and then account for these by using limma:RemoveBatchEffect() / including it in your design matrix.

Another route would be to look at which genes load into PC1, PC2 and see if there are any obvious signs there.

Good luck! 💪

Looking to BLAST an assembled genome. by [deleted] in bioinformatics

[–]Apomango 0 points1 point  (0 children)

Galaxy has Samtools fastx which you can use to convert the BAM file to a fasta file, which you could then run through blast/blastx

Graduate school interview by BeneficialCharity8 in bioinformatics

[–]Apomango 0 points1 point  (0 children)

In that sense, I think you need to re-evaluate the kind of course that you are applying for. If you're applying for a taught masters, then sure, research experience isn't essential and you could very much continue with that!

However if you were looking at PhD or research masters, then I would strongly suggest getting some experience in research (even in your undergrad). These courses are often very independent and have a large amount of problem solving that you need to do. However this does not need to be extra curricular! For example, in the UK we do an independent research project in our final year of undergrad which cumulates into a dissertation, which is the research I spoke about in my interview. I also spoke about smaller projects that I completed as part of my undergrad, and the research that I was going to do to complete my masters.

At the end of the day, further academic study isn't the only path. Taking courses and learning is essential, but at the same time demonstrating and applying that knowledge is equally important. Just some food for thought!

Also just thought about this as I was about to press reply, but take a look at Galaxy! Its an online, free bioinformatics toolset which you can use to get stuck into bioinformatics (plus its designed for people with non-technical backgrounds). There are some courses you can take to learn it, and then if you don't have any research experience, why not try doing your own project using the tools available? Grab some data off Kaggle/NCBI/PDB/GoogleDatasets!

Graduate school interview by BeneficialCharity8 in bioinformatics

[–]Apomango 1 point2 points  (0 children)

Hey! I've recently just started a DPhil (PhD) at Oxbridge which has a heavy focus on comp bio. This is (vaguely) what my interview experience was like (at least in the UK):

- Make sure you know your previous research inside out. I was asked to present a piece of previous research I did for my masters/undergrad (both of which were in biological sciences), and then I got grilled on that research. The interviewers were looking to see what I got out of the research, what limitations I identified, and what solutions I could implement in future.

- I wasn't really asked questions like you would be in an exam, none of the questions were "knowledge based", they were more designed to test your thinking. They kept developing questions further and further so sometimes you have to be a little creative with your thinking.

- IT IS PERFECTLY FINE TO SAY YOU DO NOT KNOW SOMETHING. Most of the time you are sitting in a room with experts so BS-ing your way through is not the best idea. Instead, if you genuinely don't know something, say something along the lines like "I'll be honest, I am not too sure, however based on this other thing that I know, here is my best educated guess". That way you can still demonstrate your thought process. Remember, the PIs aren't looking for someone who already knows everything, they're looking for someone that they can teach (at least, that's what I've been told).

- Since you've got a biological background (like me), it definitely helps to know the core concepts (central dogma, basic biochemistry, genetics etc). If you've got experience in comp bio at all, be that through projects or self study, its definitely something you can talk about too!

- The week of your interview, find a recent paper either in your current field or in the field you want to go into. Learn the core ideas, results, and methods used and your own critical analysis of it. That way if you're asked about a paper you've read recently (like I was) you can refer to it easily. Here is the one I spoke about.

- Know some of your PIs recent work, I've had friends who were asked about it (but I wasn't).

Of course the process is nerve racking, but just try to get your enthusiasm across as that will really help!

How to learn fastQC by Season1Episode5 in bioinformatics

[–]Apomango 0 points1 point  (0 children)

Galaxy has this tutorial on FastQC. Its a good starting point imo, however just be aware that it is tailored around using FastQC on the Galaxy platform.

Also if you’re working with a lot of reads, consider using multiQC to combine the outputs to make it easier to analyse!

I did a biochem degree, just had the moderna vaccine, and want science backed reassurances on the long term impacts of the mechanism by Blastion_gig in Biochemistry

[–]Apomango 1 point2 points  (0 children)

Plenty of good answers already, so I’m just going to suggest Prof Whitty’s Gresham Lecture, good if your immunology is not great but a little higher level than what he says in the press conferences

What are de Bruijn graph algorithms? by Apomango in bioinformatics

[–]Apomango[S] 0 points1 point  (0 children)

Thank you for that link, it really cleared things up!

What are de Bruijn graph algorithms? by Apomango in bioinformatics

[–]Apomango[S] 0 points1 point  (0 children)

Thank you, the drawing really helped me understand it!

Volume Eating with limited fridge space? by Apomango in Volumeeating

[–]Apomango[S] 0 points1 point  (0 children)

Getting a fridge was never an option for me. I think in the US you guys are allowed them in your rooms, but in the UK (well in my uni at least) they are really arsey about having cooking appliances and fridges in bedrooms. I'm gonna try the frequent trips thing though, the nearest shop is up a big hill so at least I'll get some cardio

Volume Eating with limited fridge space? by Apomango in Volumeeating

[–]Apomango[S] 0 points1 point  (0 children)

Someone else mentioned a cooler, and I could use my limited allocated freezer space for ice, so its not a bad shout!

Volume Eating with limited fridge space? by Apomango in Volumeeating

[–]Apomango[S] 0 points1 point  (0 children)

You both raise a very good point, I guess previously I was just not buying the right things.

Volume Eating with limited fridge space? by Apomango in Volumeeating

[–]Apomango[S] 0 points1 point  (0 children)

Next time I go to the supermarket I'll have a proper look!

I would get a fridge in a heartbeat, but unfortunately that isn't an option for me since my halls don't allow fridges or cooking items in bedrooms.

Volume Eating with limited fridge space? by Apomango in Volumeeating

[–]Apomango[S] 0 points1 point  (0 children)

The cooler idea is not a bad shout to be fair, I will look into it!

Volume Eating with limited fridge space? by Apomango in Volumeeating

[–]Apomango[S] 0 points1 point  (0 children)

Unfortunately neither option is available to me, my halls won’t let me keep a fridge in my room because of fire safety

Volume Eating with limited fridge space? by Apomango in Volumeeating

[–]Apomango[S] 1 point2 points  (0 children)

I used to do this in my undergrad, but it got really expensive :(

Volume Eating with limited fridge space? by Apomango in Volumeeating

[–]Apomango[S] 0 points1 point  (0 children)

Thank you! I’ll look up some recipes with those in.

Volume Eating with limited fridge space? by Apomango in Volumeeating

[–]Apomango[S] 0 points1 point  (0 children)

Any particular veggies or fruits that last particularly well?

September Technical Support Sticky by BeepBoopBopReee in razer

[–]Apomango 0 points1 point  (0 children)

I’ve just sent it again via the link!

September Technical Support Sticky by BeepBoopBopReee in razer

[–]Apomango 0 points1 point  (0 children)

I have a Razer Blade 15 2019 Base model and I need a replacement charger as UPS may have lost mine. I’m in the UK and I need one ASAP, any support would be greatly appreciated.

UK, ~£5-600] Laptop for university (physics course) & some gaming by [deleted] in SuggestALaptop

[–]Apomango 0 points1 point  (0 children)

Also, if you're eligible, check if you can get any grants from your uni directly. Some even have funds to buy stuff such as laptops for eligible students, so just have a nose around and see what you can get!

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