r/bioinformatics Dec 31 '24

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

181 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 1h ago

technical question Nextflow Resources for beginner

Upvotes

Hi everyone,

I am a graduate student in bioinformatics with experience in RNA-seq, scRNA-seq, and other omics analyses, but I am completely new to Nextflow.

I would like to learn Nextflow so I can start building reproducible pipelines and become more familiar with a tool that is widely used in industry.

There are many tutorials and videos online, but I am not sure where to begin. Are there any resources you would recommend, preferably in a specific learning order?

Thanks!


r/bioinformatics 13m ago

technical question Perturbed gene is dropped from ~70% of training examples in scGPT's perturbation prediction tutorial

Thumbnail gallery
Upvotes

tldr: if you're using/benchmarking scGPT for perturbation response prediction, be aware there's a sampling bug in their tutorial code.

I was reproducing scGPT's perturbation response prediction and found that the gene subsampling step doesn't guarantee the perturbed gene stays in the input. With the default max_length ~ 1353 and ~5000 highly variable genes, the perturbed gene gets dropped from roughly 70% of training examples. The model sees a perturbed cell's input as if it were unperturbed, while the target is still the perturbed profile.

Checked this on Norman, Adamson, and Replogle K562 and I was able to reproduce the paper's reported numbers.

My fix is to keep the perturbed gene(s) and subsample the rest to fill max_length. Surprisingly, the effect on final metrics was mixed and dataset-dependent: clear improvement on Replogle K562, roughly unchanged on Adamson, and mixed on Norman. My current read is that the standard PRP metrics don't strongly reward using the perturbed gene's identity. Curious what you think and whether you have run into something similar


r/bioinformatics 18m ago

technical question Anyone interested in learning bioinformatics through diabetes-related projects?

Upvotes

Hi everyone,

I'm an MSc Bioinformatics student with a strong interest in computational diabetes research. I'm currently learning RNA-seq analysis, transcriptomics, comparative genomics, and related bioinformatics workflows.

I'm looking for people who are also interested in learning and working on small, open-source, portfolio-style projects in bioinformatics related to diabetes. The idea is to learn together, discuss methods, analyze public datasets, and improve our skills—not to publish immediately or work on anything commercial.

I'm still learning myself, so I'd especially appreciate hearing from anyone with more experience who'd be willing to occasionally review our approach, point out mistakes, or suggest better practices. Even a bit of guidance would be incredibly valuable.

If you're interested in collaborating or mentoring informally, feel free to comment or send me a DM.

Thanks!


r/bioinformatics 5h ago

academic Seeking multiplex IF researchers for the OcupathIF Early Access Program

Thumbnail
1 Upvotes

r/bioinformatics 10h ago

technical question Discrepancy between STRING enrichment analysis and Gene Ontology Database

2 Upvotes

Hi all! I am doing some protein-protein interaction analysis on a set of genes for my undergraduate research project. I used STRING for this. STRING enrichment analysis identified that GO:0000118 (Histone Deacetylase Complex) was functionally enriched, and that 8 genes had this GO annotation.

However, when manually searching the Gene Ontology database, I found that one of the genes that STRING identified, pht1, was not annotated with this GO term.

I'm quite confused about this, am I misunderstanding how STRING gene enrichment works? Would appreciate any advice :)


r/bioinformatics 12h ago

academic Building a Python/Ilastik pipeline for Expansion Microscopy (ExM)

1 Upvotes

Hello bioinformaticians!

I'm a high school student planning to pursue bioinformatics in university. For my graduation project, I'm analyzing Expansion Microscopy (ExM) 2D data targeting SON protein in nuclear speckles (+-4x expansion factor).

I’ve set up a working Python pipeline and would love to get a check from experienced ones, as well as any tips on what to watch out for.

Done so far:

  1. Data: Wrote a Python script using raw binary reading to reconstruct 16-bit multi-channel TIFF headers.
  2. Segmentate: Using Ilastik to generate probability maps exported as .h5.
  3. Quantification: Built a Python script (h5py, scikit-image, pandas) that:
    • Thresholds the probability maps.
    • Performs connected component labeling.
    • Converts pixel counts to biological area taking into account physical pixel size and the expansion factor.
    • Extracts centroids, object counts, and fluorescence intensities into CSV format.

Are there common traps when scaling 2D pixel metrics to physical units in ExM (e.g. local distortion edge cases)?.

What additional spatial or morphological metrics are usually expected (e.g. nearest-neighbor distance, eccentricity, spatial clustering)?

Any other tips will be appreciated


r/bioinformatics 1d ago

technical question PCA high variance in PC1

Thumbnail gallery
15 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 18h ago

technical question Interaction screening with alphafold3 or similar models

1 Upvotes

Hi all,

Had an idea recently to do an interaction screen of one of our proteins of interest with proteins expressed in a certain cell type. This is obviously gonna be a large amount of proteins. I’ve seen some papers do similar things, but wanted to ask if anyone had any ideas on these sorts of workflows, specifically with regards to reducing runtimes (and thereby costs)

Specifically:

Any similar models that are significantly faster to run and have a similar accuracy?

How fast is MSA generation generally using sharding. Any other workflows that are significantly faster and still give good MSAs?

Thanks everyone!


r/bioinformatics 1d ago

technical question How to make reprodcible workflows

5 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 22h ago

academic About modelling electron transfer proteins and potential values

0 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 1d 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 1d 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 2d ago

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

5 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 2d ago

technical question Batch effect correction

5 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 2d 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 2d 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 2d 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 2d 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 3d ago

job posting Senior DevOps / Platform Engineer

11 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 3d 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 4d ago

other Resources for understanding NGS pipeline outputs

4 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 4d ago

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

5 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 5d ago

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

7 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?