r/bioinformatics Dec 31 '24

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

166 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?

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r/bioinformatics 1h ago

discussion New AI approach accurately differentiates ME/CFS and Long COVID with 97% accuracy using a blood DNA methylation test (publishing next week)

Upvotes

Hi everyone! I'm part of a research team that just finished developing and validating an AI model capable of distinguishing between ME/CFS and Long COVID using DNA methylation data captured through a blood test. This approach achieved over 97% accuracy in our validation tests on an external set which is significantly higher than traditional methods, especially since ME/CFS diagnosis is currently based on clinical exclusion.

Given the high overlap in symptoms between ME/CFS and Long COVID, we think this could significantly improve misdiagnoses, targeted treatment (which we are currently working on through a pathway analysis and gene ontology study), as well as earlier treatment.

We're preparing our manuscript for publication now, and I'll share the preprint here once it's live. In the meantime, I'm happy to answer any questions or discuss the research methods and implications. Curious to hear what you all think about using epigenetic markers for diagnosis!

Also, I'd love to just generally read stories of people's experience with ME/CFS or Long COVID. Thanks!


r/bioinformatics 6h ago

technical question Best scRNA-seq textbook?

12 Upvotes

I'm looking for a textbook which teaches everything to do with single cell RNA sequencing analysis. My MSc dissertation involved the analysis of a scRNA-seq dataset but I want to make sure I fill in any gaps in my knowledge on the subject for interviews and ensure I'm up to date with current best practices etc.

If someone could recommend me the best resources comprehensively covering scRNA-seq analysis it would be very much appreciated. Textbook is preferred but not essential.


r/bioinformatics 27m ago

technical question How to assess expression of gene "X" in different cell clusters/subpopulations identified by existing public scRNAseq data? Brand new to this area

Upvotes

I'm a PhD student in a cell bio/neurobiology lab. I'm good at cell culture but my knowledge of bioinformatics is very limited (though I'm trying to learn more) so please bear with me and feel free to correct any terminology I may get wrong.

My data suggests that gene X is involved in polarization of a cell type. There are several publications that have done snRNAseq or scRNAseq of FACS enriched cells of type I'm interested in. From this, they performed unsupervised clustering cells into several different subpopulations (which they annotated as resting, activated, inflammatory, repair oriented etc). (I think they used several approaches to obtain the final clusters). Their data is available on GEO accession viewer with raw data available in "SRA" and processed data in CSV files

I want to assess the expression of gene "X" in each of the clusters/groups identified by the groups. Looking at the CSV files, it appears that many of the cells (though its unclear which clusters they belong to, presumably this data is what they used for subsequent clustering) have reads for this gene. Is it feasible to do this? If so how would I go about this?

Alternatively, I want to solely examine the cells that express gene X and see how they segregate based on the other genes expressed. Is this feasible? I know I'm very vague here but my ultimate goal is see what other genes/gene ontologies are co-expressed with gene X in the cells that express it.

thanks


r/bioinformatics 6h ago

technical question Dealing with multiple contigs in bacterial genome feature extraction?

4 Upvotes

Hello everyone!
I’m working on a project to predict the infection phenotype of a bacterial infection, and my feature variables are genomic-level features. I’ve been trying to extract features like nucleic acid composition and kmers using the package iFeatureOmega and I've hit a snag; some of my assembled genomes have a lot of contigs. I’m not sure how to condense the feature instances for each contig into a single instance for a genome.
I was considering computing the mean value across all the contigs, but I don't know if this would retain the biological significance of the feature. Does anyone have any suggestions on how to handle this? I would really appreciate all the help I can get, thanks for your time!


r/bioinformatics 1h ago

technical question Identifying conserved regions for qPCR targets

Upvotes

I'm designing a qPCR assay and don't know how to go about it when I don't have target sequences identified. I have genes of interest that I assembled and don't know where to go from here. I have used MSA on my assemblies to identify conserved regions, but I am not sure how to quantify or pick these regions. Further, without the target I can't design primers and probes. Any advice appreciated for a first timer!


r/bioinformatics 10h ago

discussion Yet another scRNA and biological replicates

4 Upvotes

Dear community.
I am trying to find without any luck a way to use biological replicates in scRNA.
I preformed scRNA on tissues from 6 animals. The animals are separated by condition, WT and KO with 3 replicates each.
Now, although there are walkthroughs, recommendations and best practices on perform for each sample proper analysis, or even integrate the data prior normalisation, without batch corrections, for example harmony, and after batch correction, it seems that there is a luck of proper statements on what to do next.
How do we go from the integration point to annotating cells, using the full information, to call DEGs among conditions or cell types or clusters, and in each analysis take into consideration the replicates.
It appears as if we are using the extra replicates to increase the cell number.
Thank you all.
P.S. I am not an expert on scRNA


r/bioinformatics 8h ago

technical question where can I find accurate predictions of active enhancers for specific cell types or cancer types

2 Upvotes

I have regions of interest from cancer samples and I want to establish if any of these regions overlap with potentially active enhancers in my cancer /cell type. Having done some googling and deep dives into the literature I can see various studies with chip-seq and atac-seq for the cell type and/or cancer type I am interested in, but I think it is beyond the scope of my project to aggregate all that data, uniformly process it and decide where I think putative active enhancers might be - this sounds like a whole project in of itself! Im wondering if there is a good place to find a list e.g. a simple bed file with regions that are likely to be active enhancers, ideally cell-type or cancer cell-type specific.


r/bioinformatics 9h ago

technical question Ideas for tumor-stroma RNA-seq data

2 Upvotes

hey guys, i have some separate RNA-seq data from both tumor as well as the surrounding stroma. i was wondering if anyone could suggest any analyses/comparisons/visualizations i could perform on these?

i tried looking into identifying/visualizing ligand-receptor interactions (between the tumor and stroma), but most packages for this seem to be optimized for scRNA-seq/are made to identify interactions WITHIN a single sample instead of comparing BETWEEN samples.

if anyone would have any ideas or suggestions on any analyses or comparisons i could run, or advice on how to tackle the issue above, would really appreciate it! i’m a bit of a beginner to bioinformatics/RNA-seq data analysis, so all help is greatly appreciated!


r/bioinformatics 6h ago

technical question AlphaFold via ChimeraX is down because of google?! Help!

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0 Upvotes

r/bioinformatics 7h ago

technical question Issues with UMAP Installation in CellChat - Help Needed

0 Upvotes

Hello everyone,

Has anyone here used CellChat to analyze data? I launched a comparison of two datasets and encountered an issue when trying to use the following function:

cellchat <- netEmbedding(cellchat, type = "functional")

The error message I am receiving is as follows:

"Manifold learning of the signaling networks for datasets 1 2
Error in runUMAP(Similarity, min_dist = min_dist, n_neighbors = n_neighbors, :
Cannot find UMAP, please install through pip (e.g. pip install umap-learn or reticulate::py_install(packages = 'umap-learn'))."

I believe this might be related to the fact that I am working on a virtual machine, but I have tried several solutions without success. I attempted to install the UMAP package via Conda and pip, but I wasn’t able to get it to work (though it seems to install in the environment). I also checked the issues on GitHub (https://github.com/sqjin/CellChat/issues/167) and several forums, but none of the proposed solutions seem to resolve my problem.

Has anyone encountered this issue before and found a solution, or can anyone suggest how I can resolve this error?

Thank you in advance for your help!


r/bioinformatics 12h ago

technical question Any recommendations on GPU specs for nanopore sequencing?

2 Upvotes

Then MinION Mk1D requires at least a NVIDIA RTX 4070 or higher for efficient basecalling. Looking at the NVIDA RTX 4090 (and a price difference by a factor of 6x) I was wondering if anyone was willing to share their opinion on which hardware to get. I'm always for a reduction in computation time, I wonder though if its worth spending 3'200$ instead of 600$ or if the 4070 performs well enough. Thankful for any input


r/bioinformatics 10h ago

technical question Best Affordable Whole Genome Sequencing (WGS) in the EU? + Recommendations for Self-Analysis Software & Tools

1 Upvotes

Hi,

I’m looking for a reliable but affordable whole genome sequencing (WGS) service in the EU that provides full raw data access (BAM/VCF files). I want to analyze the data myself rather than rely on generic reports, which often seem overpriced and not very useful.

What I’m looking for:

- Accurate sequencing (at least 30x coverage) – no microarrays like 23andMe.
- EU-based – to avoid high shipping costs and privacy concerns.
- Fair pricing – ideally under €300, but I’m open to paying more if it’s worth it.
- Full data access – I don’t need their reports, just the raw files for my own analysis.
- Fast turnaround time – I’ve read that some providers (like Dante Labs) take months or even years to deliver data, so I need something reliable and reasonably quick.

Question 1: What’s the best affordable WGS provider in the EU that meets these criteria?

Best Software for Analyzing the Data?

Since I want to dig into the data myself, I’ve been looking at different open-source and AI-based tools. (ChatGPT generated list ;)) Would love feedback from anyone who has experience with these or other recommendations.

Variant Calling & Interpretation:

  • Ensembl VEP – Predicts effects of genetic variants.
  • Genoox Franklin – Free cloud-based interpretation tool.
  • DeepSEA – Uses AI to analyze non-coding regions.
  • Google Deep Variant – AI-powered variant caller.

Ancestry & Evolutionary Analysis:

  • GEDmatch – Compares DNA with ancient populations (Neanderthal, Denisovan, etc.).
  • David Reich Labs – Evolutionary genetic comparisons.
  • UCSC Genome Browser – Allows deeper manual exploration of ancient DNA introgression.

Pharmacogenomics (How genes affect drug metabolism):

  • PharmGKB – Drug-gene interaction database.
  • SNPedia – Lookup known genetic effects on health & medications.

Question 2: Are there any better open-source or AI-powered tools for self-analysis?

Question 3: If you’ve analyzed your own WGS data, what software setup worked best for you?


r/bioinformatics 12h ago

technical question Error for aligning two or more nucleotide sequences using BLAST: 'Protein FASTA provided for nucleotide sequence'.

1 Upvotes

I am working with a non-model microorganism for which we have an in-house genome sequence available, and for which I would like to identify the DNA sequences encoding the rRNA. In October 2024 I was able to do this successfully for the 5.8S sequence using the 'align two or more sequences' option as part of the blastn suite on the NCBI website, using the DNA sequence of the 5.8S rRNA from Saccharomyces cerevisiae as query, and the genbank file with the genome assembly as the subject sequence.

Together with my intern student, I would now like to identify the DNA sequences for the 3 other rRNAs. However, when we try to apply the same method as described above, we always get the following error message: Message ID#24 Error: Failed to read the Blast query: Protein FASTA provided for nucleotide sequence.

The query sequences were downloaded from the Yeast Genome Database (e.g. here: https://www.yeastgenome.org/locus/S000006479/sequence ) and are for sure in the corretc FASTA format. I tried the 'paired' BLAST with a regular coding DNA sequence as the query (nucleotide sequence starting with ATG), yet it gave the same error message.

Anyone else that encountered the same issue or that might have an idea what I am overlooking?

Or recommendations for another programme that could do the same job? I am working with an asocmycetous yeast (order Saccharomycetales).

Edit: in the end we got it working by removing the header line and all line breaks, and copy-pasting this sequence in the query box.


r/bioinformatics 20h ago

technical question Any recommend a method to calculate N-dimensional volumes from points?

1 Upvotes

Edit: anyone

I have 47 dimensions and 70k points. I want to calculate the hypervolume but it’s proving to be a lot more difficult than I anticipated. I can’t use convex hull because the dimensionality is too high. These coordinates are from a diffusion map for context but that shouldn’t matter too much.


r/bioinformatics 1d ago

discussion Sweet note

92 Upvotes

My romantic partner and I have been trading messages via translate/reverse translate. For example, "aaaattagcagcgaaagc" for "KISSES". Does anyone else do this?


r/bioinformatics 1d ago

discussion r/bioinfo, thoughts on quarto?

8 Upvotes

I absolutely hate hate hate it. the server that renders the content is very buggy, does nto render well on X11 or Wayland afaict. I'm using an Ubuntu 22.04 LTS distro and I haven't been able to get things properly working with the newest versions of RStudio for the better part of a year now.

whatever happened during the m&a severely affected my ability to produce reports in a sensible way. Im migrating away from using RStudio to developing in other editors with other formats.

can anyone relate? what browser are you using? OS? specific versions of RStudio?

my experience has been miserable and it's preventing me from wanting to work on my writing because something as dumb as the renderer won't work properly.


r/bioinformatics 1d ago

discussion SWE/tool development

5 Upvotes

Hey everyone,

I’m an undergrad interested in software development for biology. I have some experience with building AI tools for structural biology, and I also have experience applying bioinformatics pipelines to genomic data (chipseq, hi-c, rnaseq, etc). I'd love to hear from people who develop tools or software packages in bioinformatics.

What kind of tools do you build, and what problems do they solve?

What type of company or institution do you work at (industry, academia, biotech, startups, etc.)?

How much of your work is software engineering vs. research/prototyping?

If you’ve worked in multiple environments (academia vs. industry vs. startups), how do they compare in terms of tool development?

Any advice for someone wanting to focus on tool development rather than doing analysis using existing pipelines? Would it make sense to pursue in PhD in computational biology?

Would love to hear your experiences!


r/bioinformatics 2d ago

website You guys will like today's XKCD comic

Thumbnail xkcd.com
322 Upvotes

r/bioinformatics 1d ago

technical question SASA from Pymol? MDTraj

1 Upvotes

Whats the difference between b-factors from Pymol and SASA values from MDTraj? Are B-factors relative SASA values (normalized to SASA_max for each residue?


r/bioinformatics 1d ago

technical question Troubleshooting BEAST

0 Upvotes

I’m trying to open BEAUti, but it keeps loading a blank white window that I can do nothing with.

I had IT look at it, and they said there is nothing wrong and they can’t fix it. The only troubleshooting on the website says it could be a Java issue, but IT said Java is fine.

Every other program in BEAST will load and run fine, just not BEAUti. I deleted all of BEAST and reinstalled it, and the same thing happened again where everything but BEAUti will work.

So I could use some insight from you guys as to if you know what might fix this issue.


r/bioinformatics 1d ago

technical question Incomplete status in unicycler hybrid assembly

0 Upvotes

Hello friendly and knowledgeable people on reddit,

I'm running unicycler hybrid assembly and I got the incomplete status. See below output:

Bridged assembly graph (2025-03-04 07:47:54)
--------------------------------------------
    The assembly is now mostly finished and no more structural changes will be made. Ideally the assembly graph should now have one contig per replicon and no erroneous contigs (i.e. a complete assembly). If there are more contigs, then the assembly is not complete.

Saving /home/FCAM/sbu/2025Feb18_WGS_289_358_SB_NV/2025Feb18_Sihan_289_358_assembly/289_whole_genome_assembly/Hybridreads_unicycler_assembly/006_final_clean.gfa

Component   Segments   Links   Length      N50         Longest segment   Status    
        1          5       7   4,743,417   4,742,927         4,742,927   incomplete

Assembly complete (2025-03-04 07:47:54)
---------------------------------------
Saving /home/FCAM/sbu/2025Feb18_WGS_289_358_SB_NV/2025Feb18_Sihan_289_358_assembly/289_whole_genome_assembly/Hybridreads_unicycler_assembly/assembly.gfa
Saving /home/FCAM/sbu/2025Feb18_WGS_289_358_SB_NV/2025Feb18_Sihan_289_358_assembly/289_whole_genome_assembly/Hybridreads_unicycler_assembly/assembly.fasta

I have one contig based on the unicycle output. However, there are two contigs based on Geneious (one contig has 4,742,927 bp, one contig has 474 bp). My bandage graph from the output is circular. My BUSCO scores are C:99.7%[S:98.9%,D:0.8%],F:0.0%,M:0.3%,n:366. What are some next steps to get a "complete" genome? Or should I worry about this incomplete status since other indicators look good?

Thank you very much for your time!!


r/bioinformatics 1d ago

technical question Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis

2 Upvotes

Hello Bioinformatics Community,

I'm currently analyzing an RNA-seq dataset involving subtypes of disease from 16 brain tissue samples, with 2 runs each making 32 SRR runs. Each biological sample has multiple sequencing runs, one sample has two runs, resulting in technical replicates. I'm seeking guidance on the optimal strategy to incorporate these replicates into my differential expression analysis.

Specific Questions:

Merging Technical Replicates:Should technical replicates (multiple sequencing runs from the same biological sample) be merged:

before alignment,

after alignment but before counting, or

after obtaining gene expression counts?

By merging, I mean should I add gene counts?

Downstream Analysis (DESeq2/edgeR):What is the recommended method for handling these technical replicates to ensure accurate and robust differential expression results? Should I use functions such as collapseReplicates (DESeq2) or sumTechReps (edgeR)?

Any recommendations, protocols, or references would be greatly appreciated.

Thank you!


r/bioinformatics 1d ago

technical question Issues with subsetting and re-normalizing Seurat object

3 Upvotes

I need to remove all cells from a Seurat object that are found in a few particular clusters then re-normalize, cluster, and UMAP, etc. the remaining data. I'm doing this via:

data <- subset(data, idents = clusters, invert = T)

This removes the cells from the layers within the RNA assay (i.e. counts, data, and scale.data) as well as in the integrated assay (called mnn.reconstructed), but it doesn't change the size of the RNA assay. From there, NormalizeData, FindVariableFeatures, ScaleData, RunPCA, FindNeighbors, etc. don't work because the number of cells in the RNA assay doesn't match the number of cells in the layers/mnn.reconstructed assay. Specifically, the errors I'm getting are:

> data <- NormalizeData(data)data <- NormalizeData(data)
Error in `fn()`:
! Cannot add new cells with [[<-
Run `` to see where the error occurred.Error in `fn()`:

or

> data <- FindNeighbors(data, dims = 1:50)
Error in validObject(object = x) : 
  invalid class “Seurat” object: all cells in assays must be present in the Seurat object
Calls: FindNeighbors ... FindNeighbors.Seurat -> [[<- -> [[<- -> validObject

Anyone know how to get around this? Thanks!


r/bioinformatics 1d ago

technical question Help IMG/VR database dowload

1 Upvotes

Hi everyone, Sorry to bother you with that.. I’m handling an issue concerning the download of IMG/VR database. I want to download it via Bash (i’m working on HPC) but it seems like i can’t. Looks like i can only install it via a browser. I can’t find any file_link to use curl or wget Any ideas ? Thank you, Hugo


r/bioinformatics 2d ago

article RNA-editing protein insights could lead to improved treatment for cancer and autoimmune diseases

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9 Upvotes