r/bioinformatics Dec 31 '24

meta 2025 - Read This Before You Post to r/bioinformatics

182 Upvotes

​Before you post to this subreddit, we strongly encourage you to check out the FAQ​Before you post to this subreddit, we strongly encourage you to check out the FAQ.

Questions like, "How do I become a bioinformatician?", "what programming language should I learn?" and "Do I need a PhD?" are all answered there - along with many more relevant questions. If your question duplicates something in the FAQ, it will be removed.

If you still have a question, please check if it is one of the following. If it is, please don't post it.

What laptop should I buy?

Actually, it doesn't matter. Most people use their laptop to develop code, and any heavy lifting will be done on a server or on the cloud. Please talk to your peers in your lab about how they develop and run code, as they likely already have a solid workflow.

If you’re asking which desktop or server to buy, that’s a direct function of the software you plan to run on it.  Rather than ask us, consult the manual for the software for its needs. 

What courses/program should I take?

We can't answer this for you - no one knows what skills you'll need in the future, and we can't tell you where your career will go. There's no such thing as "taking the wrong course" - you're just learning a skill you may or may not put to use, and only you can control the twists and turns your path will follow.

If you want to know about which major to take, the same thing applies.  Learn the skills you want to learn, and then find the jobs to get them.  We can’t tell you which will be in high demand by the time you graduate, and there is no one way to get into bioinformatics.  Every one of us took a different path to get here and we can’t tell you which path is best.  That’s up to you!

Am I competitive for a given academic program? 

There is no way we can tell you that - the only way to find out is to apply. So... go apply. If we say Yes, there's still no way to know if you'll get in. If we say no, then you might not apply and you'll miss out on some great advisor thinking your skill set is the perfect fit for their lab. Stop asking, and try to get in! (good luck with your application, btw.)

How do I get into Grad school?

See “please rank grad schools for me” below.  

Can I intern with you?

I have, myself, hired an intern from reddit - but it wasn't because they posted that they were looking for a position. It was because they responded to a post where I announced I was looking for an intern. This subreddit isn't the place to advertise yourself. There are literally hundreds of students looking for internships for every open position, and they just clog up the community.

Please rank grad schools/universities for me!

Hey, we get it - you want us to tell you where you'll get the best education. However, that's not how it works. Grad school depends more on who your supervisor is than the name of the university. While that may not be how it goes for an MBA, it definitely is for Bioinformatics. We really can't tell you which university is better, because there's no "better". Pick the lab in which you want to study and where you'll get the best support.

If you're an undergrad, then it really isn't a big deal which university you pick. Bioinformatics usually requires a masters or PhD to be successful in the field. See both the FAQ, as well as what is written above.

How do I get a job in Bioinformatics?

If you're asking this, you haven't yet checked out our three part series in the side bar:

What should I do?

Actually, these questions are generally ok - but only if you give enough information to make it worthwhile, and if the question isn’t a duplicate of one of the questions posed above. No one is in your shoes, and no one can help you if you haven't given enough background to explain your situation. Posts without sufficient background information in them will be removed.

Help Me!

If you're looking for help, make sure your title reflects the question you're asking for help on. You won't get the right people looking at your post, and the only person who clicks on random posts with vague topics are the mods... so that we can remove them.

Job Posts

If you're planning on posting a job, please make sure that employer is clear (recruiting agencies are not acceptable, unless they're hiring directly.), The job description must also be complete so that the requirements for the position are easily identifiable and the responsibilities are clear. We also do not allow posts for work "on spec" or competitions.  

Advertising (Conferences, Software, Tools, Support, Videos, Blogs, etc)

If you’re making money off of whatever it is you’re posting, it will be removed.  If you’re advertising your own blog/youtube channel, courses, etc, it will also be removed. Same for self-promoting software you’ve built.  All of these things are going to be considered spam.  

There is a fine line between someone discovering a really great tool and sharing it with the community, and the author of that tool sharing their projects with the community.  In the first case, if the moderators think that a significant portion of the community will appreciate the tool, we’ll leave it.  In the latter case,  it will be removed.  

If you don’t know which side of the line you are on, reach out to the moderators.

The Moderators Suck!

Yeah, that’s a distinct possibility.  However, remember we’re moderating in our free time and don’t really have the time or resources to watch every single video, test every piece of software or review every resume.  We have our own jobs, research projects and lives as well.  We’re doing our best to keep on top of things, and often will make the expedient call to remove things, when in doubt. 

If you disagree with the moderators, you can always write to us, and we’ll answer when we can.  Be sure to include a link to the post or comment you want to raise to our attention. Disputes inevitably take longer to resolve, if you expect the moderators to track down your post or your comment to review.


r/bioinformatics 7h ago

technical question PCA high variance in PC1

Thumbnail gallery
6 Upvotes

Hi everyone,

I'm analyzing pseudobulk data generated by summing gene expression across cells from different samples profiled with a spatial imaging platform. When I perform PCA on the pseudobulk matrix, PC1 explains an unusually large proportion of the total variance. In addition, all of the PC1 loadings are positive, which I also think is unusual.

Does this indicate a systematic technical bias (I have looked for differences in sequencing depth or cell numbers)? Or are there biological scenarios where this pattern would be expected? These are samples from malignant tissue.


r/bioinformatics 46m ago

academic About modelling electron transfer proteins and potential values

Upvotes

Dear Reddits,

I have some experience with bioinformatics in general (I can open my Linux command line and feel I'm in The Matrix; it is very popular on Instagram, actually), but I don't know anything about modeling. I would like to know if it's SIMPLE (probably not) to determine the potential value (E value) of certain electron transfer proteins. I know AlphaFold can give you some kinda cool model, but I need to know if there is an easy way, or even a way, to just get the E value. Even if it's a not-so-realistic approximation, it would be nice. If it's going to take me more than 1 week, I pass. However, it might be good to know for future endeavors.
That
XOXO


r/bioinformatics 8h ago

technical question Handling GWAS independence issue?

1 Upvotes

I'm running an annotation/enrichment analysis on a GWAS study, and I'm sort of a bit lost/confused on something.

Originally, I only filtered the GWAS study for genome-wide significant variants using a standard p-value threshold, and also used LD-clumping to identify genomic loci.

However, it was also pointed out to me that these variants may not be independent, and that a single association signal may be represented many times, potentially leading to inflation in statistical significance.

I'm sort of unsure how to handle this. I tried a locus-pruning method which gave me way less variants and pretty poor coverage on my study and rendering a lot of my downstream analysis mute. I'm also confused since I haven't seen a lot of similar papers use this kind of filtering method. I did run LDSC too, and most of my findings were insignificant so it did kind of handle the genomic independence part. But I'm still not sure what the best practice is here.


r/bioinformatics 8h ago

technical question How to make reprodcible workflows

0 Upvotes

Hi, so I am a undergrad working in a computational biology or molecular biology lab. For next semester my new project is in large part to create reproducible workflows/code and lab manuals for our lab. I taught myself to code and what i have on my laptop is... disorganized to say the least. I should learn how to do this. Currently I largely code using gemini and then tweak anywhere from most of to 25% of the code it writes. I almost always use hard coded paths if i can. Does anyone have any advice for where I could learn something like this, a textbook or website?

For context, my last project was to use AutoDock Vina for screening of 770,000 molecules I carefully downloaded and cleaned from ZINC database to 310,000. This library was based on previous experimental results on a new protien we are targeting in fungi. I also selected a new protien conformation to target based on some major errors in the protien the lab was using and a bunch of literature review. My next step will be to test against Dock6, a diffrent type of scoring algorithm. I wrote all of my own scripts for this and I imagine my first task will be to get them reproducible for another person to use.


r/bioinformatics 20h ago

website Tss/softberry

0 Upvotes

Well, for my project, I was going to use softberry tssplant, but apparently the site is down. Does anyone know of an alternative way to find TSS in genome sequences?


r/bioinformatics 1d ago

technical question What are the current standard for 3D Protein Structure Comparison between proteins?

4 Upvotes

I have characterized a peptidase domain of a large multidomain containing protein. I was able to clone just the peptidase domain in a construct for assays. There are putative homologs (~60% sequence identity) from distantly related species. I am looking to test these candidates for activity in the same system.

I have the predicted AlphaFold structures, what is the best way to compare these 3D models? I am currently using matchmaker on chimerax. Are there some better tools?


r/bioinformatics 1d ago

technical question Batch effect correction

6 Upvotes

Hello,

I am an engineering student in applied mathematics, and as part of an internship, I am working on statistical analysis in biology.

**Context:**

I am working on an experiment conducted by three experimenters. Each experimenter has four plates (this part is not very important), with a total of six different stainings, each containing three different coatings, within which there are 40 donors.

To summarize:

**Experimenters (3) > Stainings (6) > Coatings (3) > Donors (40)**

We are working with Opera imaging plates, so we analyze DAPI, actin, and, depending on the staining, several other markers such as Granzyme B, pTyr, MTOC, etc.

**Problem:**

I quickly noticed that the data differ substantially between experimenters. One experimenter consistently has more cells than the others across all stainings.

To investigate this, I trained a simple decision tree to distinguish between experimenters. My reasoning was that if the tree can reliably identify the experimenter, then there is likely a batch effect; otherwise, there probably is not.

As expected, the experimenter with the consistently higher cell counts is identified very accurately. The other two experimenters can also be distinguished, although not to an alarming extent.

**Conclusion:**

I would therefore like to correct this bias using what biologists refer to as **batch effect correction**. However, most of the documentation I have found focuses on scRNA-seq or single-cell multiomics, which does not seem to match the type of data we have in this experiment.

Do you have any suggestions on where I should look? Any interesting papers you would recommend?

I have read papers mentioning Harmony and ComBat, but when I asked an AI, it suggested using the Python classes `ot.da.LinearTransport` and `ot.da.SinkhornTransport`.

The reported performance of these libraries looks very appealing, but I would rather not trust an AI blindly, so I thought I'd ask for your advice instead. 🙃


r/bioinformatics 1d ago

technical question Stand alone programs for phylogenetic tree editing & visualisation?

25 Upvotes

I've been in industry for a good few years, and I'm trying to work on some old research that I never published. However, all the old programs I used during my PhD for tree editing & visualization have either been deleted or are now paid programs.

I have 0 coding knowledge and was getting by with online tools and programs other people made (i.e enterobase, galaxy, iTOL, FigTree etc) but I've been struggling to find something comparable to iTOL and FigTree for editing and visualization.
Does anyone have any recommendations?


r/bioinformatics 1d ago

technical question Undergrad Learning Single Nuclei-SEQ/Bioinformatics Part 4: Need Advice for nuclei extraction and isolation

2 Upvotes

Hi everyone, me again.

If you want context, check my previous posts. Made a similar post on lab rats, essentially reposting here.

We are going to start extracting and isolating soon. We have drafted a protocol and the tissue type we are working with are DRGs and sometimes brain. This week and over the course of the next few weeks, we are going to start isolating and optimizing our protocol. We have maybe around 15 tries or runs to get it right consistently before we start working with real tissue (non practice tissue, tissue that has the pathology induced.)

Any tips, advice or generally useful info I should know? What should I expect?

Thank you and any help would be appreciated!

- Undergrad P_T67


r/bioinformatics 1d ago

technical question Issue in interpreting Unique gene using Panaroo

1 Upvotes

I collected genome assemblies for my species from NCBI and ran a pan-genome analysis using Panaroo. One gene cluster was identified as unique in my target strain, but when I ran BLASTp on that sequence, it showed a hit in another strain that is not listed in the current NCBI genome database.

I am trying to understand how to interpret this result. Does this mean the gene is not truly unique to the species, or could it still be considered unique if that strain is an unsubmitted / uncurated genome?

What is the best way to determine whether this gene is genuinely unique to the species, or only unique within the genomes available in NCBI?


r/bioinformatics 1d ago

technical question How should I dock a peptide containing a custom covalent linker/staple?

1 Upvotes

I have a custom peptide with a custom linker in an SDF file. How can I dock it to a protein receptor while preserving the linker?


r/bioinformatics 2d ago

job posting Senior DevOps / Platform Engineer

12 Upvotes

At the Diagnostic and Research Institute of Human Genetics, Medical University of Graz, our bioinformaticians define the diagnostic data-analysis logic that can change patients' lives. We're looking for an experienced DevOps professional to make these systems secure, maintainable and reliable.

📍Graz, Austria | Full-time | 1 remote day/week | Relocation welcome

Your mission:

  • Design end-to-end pipeline and deployment architecture with bioinformatics and IT teams
  • Build CI/CD, automated testing, versioning, deployment, release and rollback processes
  • Automate workflows with Python, Linux/Unix shell and Windows PowerShell
  • Strengthen monitoring, logging, incident response and documentation
  • Critically review human- and AI-assisted code for quality and security
  • Contribute expert input in pipeline design meetings

Your profile:

  • Master's + 5 years, or Bachelor's + 7 years of DevOps/platform experience
  • Strong Linux and Windows production experience, systems integration
  • Expert Python automation; strong shell scripting and PowerShell
  • Solid Git, CI/CD and release-management background
  • Virtualization/containerization experience
  • Advanced English or German

💶 Compensation: According to the Austrian Collective Agreement for University Staff (Kollektivvertrag für Universitätspersonal); classification and possible overpayment depend on education, qualifications and relevant experience.

Interested? Send your CV and a short motivation letter to Benjamin Spiegl: [[email protected]](mailto:[email protected])
Optional: GitHub/GitLab or anonymized code/architecture examples welcome.


r/bioinformatics 2d ago

technical question Use of Msigdb: conversion between human and mouse

1 Upvotes

Hi all,

I am just curious about the use of the human and mouse sets from the Msigdb. Between using the mouse MSigDB directly and using human MSigDB with ortholog mapping to mouse, would there be much difference? Or, asking a different way, are there any advantages/disadvantages in either way?

I've read that both methods are similar but am still not really sure if they are interchangeable.


r/bioinformatics 2d ago

technical question AutoDock Vina vs ClusPro

0 Upvotes

Hi so I was exploring autodock vina and cluspro and I wanted to see which one is better for antibody docking. does anyone know the pros and cons of each. also for high school students is using cluspro completely free without like special email addresses and stuff like that?

I know about haddock and i created an account but it wouldn't allow me to enter like a project or anything like that for some reason. 🤔


r/bioinformatics 3d ago

other Resources for understanding NGS pipeline outputs

3 Upvotes

Hi everyone,

I am working on a variant calling project on my own and I am struggling to understand and interpret the output from each step. I want to know what each file and result actually means not just how to generate it.

To give a simple example, after mapping reads to the reference genome you usually run samtools flagstat. I would like to understand which lines in the output are the most important to pay attention to, what kinds of sanity checks I should be doing and what it means if a particular metric is high or low.

I have already searched through BioStars and this subreddit but I could not find answers to many of the questions I have.

If you know of any books, blogs or paper that explain how to interpret the output at each step, I would really appreciate the recommendations. Thanks!


r/bioinformatics 3d ago

discussion Proseg vs UCS cell segmentation on Xenium data (v1 nuclear expansion only, no membrane stain)

7 Upvotes

Has anyone tried both and compared results?

Based on what I've read, Cellpose prior + Baysor or Proseg + some admixture QC might be the top performing segmentation methods at the moment.

UCS is a bit newer and has yet to be included on a published benchmark.

GitHub repos for reference:

Proseg

UCS


r/bioinformatics 4d ago

technical question Reliability of AutoDock Vina, MD simulations, and ADMET filters?

9 Upvotes

Title. I am currently planning to work on an independent research project regarding drug purposing in neurodegenerative diseases. Are these approaches accurate and widely recognized in computational drug repurposing research?

Or are there any other alternatives you recommend?


r/bioinformatics 4d ago

technical question Need help in iDEP 2.0 webtools

0 Upvotes

Hi everyone, I've recently been studying how to use the iDEP 2.0 web tool to perform differential gene expression analysis.

Earlier, I successfully uploaded and analyzed my data without any issues. After that, I put my laptop to sleep while I worked on something else. When I came back and tried to upload my data again, I encountered this problem. I've tried submitting the data multiple times, but it still doesn't work.

Has anyone experienced this issue before? How can I fix it?


r/bioinformatics 5d ago

academic Travel Award Opportunity for Bioinformatics Grad Students & Postdocs (Deadline July 21)

12 Upvotes

If you're a graduate student, postdoc, medical student, or early-career researcher working in bioinformatics, genomics, AI for healthcare, computational biology, or precision medicine, this may be worth checking out.

The AGBT Precision Health Meeting is offering Next Gen Leadership Awards that cover:

  • ✅ Full conference registration
  • ✅ Hotel accommodations
  • ✅ Travel support

The meeting takes place September 14–16, 2026 at the Loews Coronado Bay Resort in San Diego and brings together researchers from academia, hospitals, biotech, and pharma to discuss topics including:

  • Bioinformatics & computational genomics
  • AI and machine learning in precision medicine
  • Multi-omics
  • Rare disease genomics
  • Clinical genomics
  • Diagnostics and translational research

If you're presenting research or planning to pursue a career in genomics or precision medicine, this is a great opportunity to meet investigators, clinicians, and industry scientists.

Application deadline: July 21 (11:59 p.m. CST)

More information and application:
https://www.agbtprecisionhealth.org/next-gen-awards

Happy to answer questions about the program if I can.


r/bioinformatics 5d ago

technical question Viewing accession numbers of histone H3 in Mega12?

0 Upvotes

If this is the wrong subreddit or an insufficiently appropriate question for this subreddit, my deepest apologies to the mods and others. Please understand, I have already searched for my answers with all my might, but given I am at a level of comprehension where I don't even know the questions I need to ask, I have reached the point of frustration where it seems reasonable to find a place to ask outright. My apologies for my lack of knowledge, I ask only in good faith.

Main Question: When viewing a .tre file in MEGA 12 of "unedited maximum likelihood single-gene trees" published alongside a study (ie, not my own files), is there anything embedded in this file that would contain the specific gene sequences used for each leaf? Or, even the GenBank accession numbers for the specific gene?

I have figured out (I think) that in constructing this tree, the authors would have had a separate file with these sequences that they aligned with MUSCLE and then imported into the tree explorer for construction and analysis (I think?). I am not sure if there is a way that this file data is still associated with the published .tre file, or can be reverse engineered somehow.

"Are the GenBank vouchers not already attached to the leaves?"

They are, but this is a weird situation. I'm not actually asking for the GenBank vouchers of the specimen. I am aware I don't know enough to word this properly, I will do my best. The tree I am viewing used the histone H3 genes of each specimen. The GenBank specimen vouchers are not enough, I need the accession numbers of each specimen's H3 gene.

Or, actually. I might not need them depending on the answer to the following:

Secondary Question: When researchers are collecting gene sequences to then align in MUSCLE, are they importing this data directly from GenBank, or is it something that has to be manually input (or at least manually copy-and-pasted)?

"Why is this distinction so important to you?"

The simplest answers is it's really incredibly important in figuring out Exactly How Badly Did This Research Team Fuck Up.

I rewrote this section three times, so I'm going to give the stupid simple explanation. A research study's supplementary table of all specimens used for genetic analysis was found to have been copy-and-pasted from its opposition's previous study without double-checking accession numbers.

I need to know for absolute certain if these incorrect accession numbers were the ones used to conduct the analyses, or if the correct genetic data was imported from elsewhere, and thus miraculously

This published study was already filled with mutually exclusive statements and errors and mislabeled figures and misrepresentations of sources, so they've already messed up enormously. I am already working on constructing a table by hand to track the vouchers they and their opposition cited across a handful of papers to pinpoint where things might have gone wrong. But I really need to understand how deeply their analytic data was affected by this because the...the implications. God, the implications.

Especially since in their most recent rebuttal, they did not address any of the allegations and actually doubled down on their claims and made further conclusions and analyses based upon their previous study. And the associated species register is very weirdly taking their side, even so far as to make updates the study didn't actually ask for. So I can't actually rely on the people who know what they're doing to double check the work for me anymore.

Apologies for the length of the post, this was actually the shortest version of that explanation. I can explain the really weird situation in more detail if needed. I understand this could likely be a situation in which the only option is to learn the process and replicate the results myself. I do intend to learn about genetic and molecular phylogeny properly at some point (likely in the near future) even if it intimidates me.

Thank you very much for your time and patience, especially since I struggle with communication and I am sure this was not pleasant to work through. And once again my sincerest apologies if I am an idiot in posting here or asking this.


r/bioinformatics 5d ago

technical question Pseudobulking inside of a cell type.

4 Upvotes

Say I am analyzing a dataset, and I already have my clustering and annotations done and provided. I am looking at a gene of interest and want to compare its biological function within a cell type by contrasting positive and negative cells for that gene. I was wondering if, after creating these 2 groups, I should drop the gene, and if so, why I should do that, and what it affects. Specifically, because I am pseudobulking between the 2 groups to see which pathways are enriched in the + versus the negative cells, to assess the potential biological difference in function between the 2. I want to make sure I am doing my analysis right and not inflating -log10p values etc, looking for advice here.

EditThe dataset I am taking has samples from 3 donors, all same part of the of the brain.


r/bioinformatics 6d ago

academic Are there computational biology / bioinformatics problems that naturally require continual learning?

26 Upvotes

Hi everyone,

I’m looking for examples of problems in computational biology or bioinformatics where continual learning (incrementally updating a model as new data arrives, without retraining from scratch) would be genuinely useful. The type of scenario I have in mind is something like this:

A model is trained on one large dataset (e.g. proteomic data from mammals). Some time later, a new dataset arrives (e.g. fish species, new sequencing technologies, newly collected patient cohorts, etc.).

We’d like to update the model to incorporate the new data without retraining from scratch, while also avoiding catastrophic forgetting of what it previously learned.

Of course, the mammals/fish example is just illustrative, I suspect there are much more compelling real-world examples.

I’m particularly interested in problems where:

* New data arrives continuously or in regular batches.

* The data distribution changes over time.

* Retraining from scratch is computationally expensive, impractical, or otherwise undesirable.

* Existing workflows currently rely on periodic retraining, but continual learning could plausibly be a better alternative.

Do any applications, datasets or benchmark come to mind? These could be in genomics, proteomics, single-cell biology, drug discovery, protein language models, medical imaging, clinical prediction, or any other area.

I’d also be interested to hear if you’ve tried continual learning in practice and found that it didn’t help, and why.

Happy to answer any clarifications about Continual Learning!


r/bioinformatics 6d ago

technical question Free energy perturbation

3 Upvotes

Does anyone have any ideas on how to set up a flat-bottom wall for forward and backward FEP? Or maybe some other type of restraint? In the ligand.

The hysteresis between the forward and backward runs for the protein-ligand leg is pretty significant. I'm getting kind of tired of running a million tests 😂

The ligand-in-water leg, though, behaved really nicely.


r/bioinformatics 6d ago

statistics Metrics for calculating similarity between different cell types in two single cell datasets ?

5 Upvotes

Hello, I am trying to calculate the transcriptomic similarity profile between two dataset across defined clusters/cell types, I was wondering what kind of metric is appropiate (e.g. spearman, pearson, cosine...), and should I just calculate for variable genes HVG or across the whole transcriptome, and if there are other considerations ?