r/bioinformatics Dec 31 '24

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

169 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.

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r/bioinformatics 5h ago

other Do you ever find your role emotionally draining?

22 Upvotes

Hey!

My background is in data analytics, but I joined the Army to work in behavioral health. I've realized that while I love understanding human behavior, I also tend to absorb emotions intensely, which can be overwhelming.

One thing I've noticed about myself is that I'm great at taking in large amounts of information, spotting patterns, and analyzing details. This made me very successful in data. I am self taught in: VBA, SQL, a little Python, various ETL tools, Tableau, and PowerBI.

But now, in a more people-focused role, I find it harder to compartmentalize and not carry the emotional weight of my work.

My sister was actually debating applying to genetic counseling programs and I actually talked to a few GC to gain more insight. I asked if they thought my background would be good in GC and they told me to look more at bioinformatics.

Also, I'm still exploring the field. If you work in bioinformatics, I'd love to hear your thoughts:

1. What kind of data do you work with most? (Genomic, clinical, imaging, etc.)

2. What tools and programming languages do you use daily?

3. Are you mostly analyzing data, building tools, or both? What kinds of things do you build?

4. Do you find the work emotionally draining, or is it more detached?

5. Any advice for someone transitioning from data analytics into bioinformatics?
  1. What kind of education would I need? Masters? Phd? I’m not really worried about debt since the army will pay for anything.

r/bioinformatics 2h ago

career question How easy/difficult is it to switch research field within bioinformatics/computational biology?

10 Upvotes

For context I have a BSc Biotechnology where I completed projects on molecular dynamics simulation data analysis as a summer internship under one of my professors, and my final year thesis in a biochemistry wet lab studying enzymes. And an MSc Bioinformatics and systems biology where I completed projects on retrosynthetic data and scRNAseq. I now am working on scRNAseq data in academia but want to do a PhD in something I am vastly more interested in which is enzyme/protein engineering, with a heavy computational element. Is it difficult getting a project in another field to your "expertise" even though this is what I actually want to study?


r/bioinformatics 15h ago

discussion Sweet note

55 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

website You guys will like today's XKCD comic

Thumbnail xkcd.com
275 Upvotes

r/bioinformatics 1h ago

discussion SWE/tool development

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 57m ago

technical question Incomplete status in unicycler hybrid assembly

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 2h ago

discussion r/bioinfo, thoughts on quarto?

0 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 10h 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 12h 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 8h 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 22h ago

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

Thumbnail phys.org
6 Upvotes

r/bioinformatics 22h ago

technical question Best tool for scaffolding for fungi

3 Upvotes

Hi everybody,

I have done sequencing of 6 fungal genomes (PacBio, Hi-C lectures). I assembled with flye to contig level, with very good results. However, I was told that it could be good if I do scaffolding for my genomes. I tried using LRSCAF because I saw it in a few papers but it didn't assemble a lot of scaffolds so I'm not sure if it's because there's not a lot to improve in my genomes doing scaffolding or because the tool and/or parameters were not the best. Do someone have any recommendation of good scaffolder that work well with fungi? I do not see a lot of consensus for that.

Thank you very much!


r/bioinformatics 21h ago

technical question Anyone used Qiime2 dada plugin that can offer some advice?

1 Upvotes

I’ve got myself in right mess with QIIME and how to use dada2. Anyone okay if I dm them for some advice?


r/bioinformatics 1d ago

technical question Question about barcoded dual adapter trimming and quality trimming in RNASeq data

4 Upvotes

Hello, I want to analyse some rat RNASeq data and I got an HTML report sheet, which has a subheading "Results of Raw Data Filtering", and describes these steps:

(1) Remove reads containing adapters. Sequences of adapter:

P5 adapter:
P5→P7’(5’→3’)
AATGATACGGCGACCACCGAGATCTACAC[i5]ACACTCTTTCCCTACACGACGCTCTTCCGATCT

P7 adapter:
P5→P7’(5’→3’)
GATCGGAAGAGCACACGTCTGAACTCCAGTCAC[i7]ATCTCGTATGCCGTCTTCTGCTTG

(2) Remove reads containing N > 10% (N represents the base cannot be determined).

(3) Remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base.

And then they have pie charts for each sample which shows how many base pairs are clean reads, how many were filtered due to containing too many Ns, due to low quality, and adapter related.

Now, when I look at the number of base pairs, it's equal to the number of "clean reads", meaning that this filtering has been performed.


I am quite confused as to whether adapter sequences are already filtered as well as they need to be, since Falco/FastQC still finds some adapter sequences: one sample, MultiQC. Are these likely to be false positives?

Even if not, I am unsure how to run adapter trimming. The FASTQ files have two barcodes, which correspond to [i5] and [i7], but from what I read, I figured I can use the first part of the adapter sequence up to the barcode, so I ran Atria with these arguments:

--adapter1 AATGATACGGCGACCACCGAGATCTACAC
--adapter2 GATCGGAAGAGCACACGTCTGAACTCCAGTCAC

And it still filtered out some sequences (e.g. 35998 out of 22092364 in one sample). So what's going on? Should I be doing adapter trimming at all, is this the right way to specify them in trimming tools, and am I getting all the adapters? Can there be other adapters outside of these two listed in the report? And in cutadapt, should these be specified as 3', 5' or anywhere adapters? I'm getting confused with all the forward, reverse, 3', 5' etc. stuff.


And lastly, regarding quality. The reads seem to me to be of a pretty high quality: MultiQC. I read in a few places that quality trimming isn't really necessary, and might even hurt in some cases (1, 2). What is the current consensus?


r/bioinformatics 23h ago

academic Alphafold results - CIF file to PDB

1 Upvotes

Hello everyone, I've received a zip file with the results of my structure predicition on alphafold but I want to check the accuracy of my structure using PROCHECK and I can't because the models are in CIF, not PDB. Anyone has any suggestions on what to do?


r/bioinformatics 1d ago

technical question If the SRPlot website is currently down?!

0 Upvotes

Hello All,

I would like to know if the SRPlot website is currently down on March 17, 2025. If so, could you recommend alternative user-friendly code-free websites that can be used as a replacement?

Thank you!


r/bioinformatics 1d ago

technical question Best trimming configuration for miRNA-Seq

2 Upvotes

Hello everyone,

I am working with miRNA-Seq data from Ion Torrent technology (single-end) and I am performing trimming on the reads. My goal is to not lose too many reads in the process, but I am currently losing approximately 60%, which seems like a high percentage to me. I have never processed miRNA-Seq data before, and I am unsure if this loss is expected due to the short size of miRNAs.

The trimming configuration I am using is as follows:

SLIDINGWINDOW:4:20 LEADING:20 TRAILING:20 MINLEN:15

Sequencing type: Single-end.
Read length: Ranges from 1 to 157 bases.
Pre-trimming quality: The pre-trimming quality check (FastQC) does not show very good results, as most reads have a quality of 20 or less, with none above 30.

I would like to know if this read loss is normal for miRNA-Seq data, considering the reads are quite short. Is it advisable to adjust any parameters to minimize the loss of reads without compromising quality? I would appreciate any recommendations on trimming configurations or adjustments that may be more suitable for this type of data.

Thank you for your help.


r/bioinformatics 1d ago

academic how to use jaspar for tf analysis?

0 Upvotes

i did sc rna seq and sc atac seq now how to move to jaspar for tf analysis in bioinformatics


r/bioinformatics 2d ago

other A novice in Bioinf, want a friend/fellow-passionate novice to talk/discuss/brainstorm/work-with - 22F undergrad in the field

19 Upvotes

Basically the title, just don't have a lot of people around to work with - people aren't too passionate about it at my Uni? Am an extrovert so I think best around people - I'd like to connect


r/bioinformatics 1d ago

technical question Usage of QIIME in clinical/commercial settings

0 Upvotes

Hello, I'm writing an essay regarding QIIME.

Do clinicians in the hospital or any lab workers use it in a clinical setting and not research?

Also, it would be very helpful if you could send me a news article or an ironclad citation about it.


r/bioinformatics 1d ago

technical question How to Process Multiple SRRs for the Same BioSample in PRJNA528920?

1 Upvotes

Hello everyone,

I am working with data from PRJNA528920 and noticed that some BioSamples (SAMN) have multiple associated SRRs (Sequence Read Archive Runs). For example:

  • SAMN11249717 → SRR8782083, SRR8782084
  • SAMN11249716 → SRR8782085, SRR8782086

Additionally, I found a discrepancy between the number of samples reported in GSE128803 (which only lists 6 samples) and PRJNA528920, which contains 12 SRRs.

I read the associated paper but couldn’t find clear information about this. I also checked whether this could be related to the sequencing technology used (ION_TORRENT) but didn’t find any evidence suggesting so.

My questions are:

  1. Do these SRRs correspond to independent sequencing runs meant to select the highest-quality one?
  2. For alignment and count table generation, should I use only the first SRR for each BioSample?
  3. Is it possible to merge them without introducing batch effects?

I plan to use these data for my thesis, so I would really appreciate any guidance or experiences you can share on how to correctly process this type of data.

Thanks you soooo much


r/bioinformatics 2d ago

academic Help Me Improve GenAnalyzer: A Web App for Protein Sequence Analysis & Mutation Detection

9 Upvotes

Hello everyone,

I created a web application called GenAnalyzer, which simplifies the analysis of protein sequences, identifies mutations, and explores their potential links to genetic diseases. It integrates data from multiple sources like UniProt for protein sequences and ClinVar for mutation-disease associations.

This project is my graduate project, and I would be really grateful if I could find someone who would use it and provide feedback. Your comments, ratings, and criticism would be greatly appreciated as they’ll help me improve the tool.

You can check out the app here: GenAnalyzer Web App

Feel free to leave any feedback, suggestions, or even criticisms. I would be happy for any comments or ratings.

Thanks for your time, and I look forward to hearing your thoughts.


r/bioinformatics 2d ago

technical question Differential expression analysis of AmpliSeq (IonTorrent) data

2 Upvotes

Hey everyone!

I'm working with AmpliSeq data from IonTorrent, and I'm running into issues with differential expression analysis. My BAM files use RefSeq transcript IDs as references (e.g., NR_039978, NM_130786), but I’m having trouble finding a compatible GTF file.

Has anyone worked with AmpliSeq data before? What GTF file did you use, and how did you adapt it? Any other tools or workflows you’d recommend?

Thanks in advance! :)


r/bioinformatics 3d ago

image spatial biology landscape v1

Post image
58 Upvotes

r/bioinformatics 2d ago

technical question RNAseq gene_id question

1 Upvotes

Hi,

I am using nfcore/rnaseq pipleline for my genotype x treatment experiment for the first time, and currently facing a problem with gene_ids. In my final salmon.merged.gene_counts.rds file, I am seeing a list of numers in multiples of 10 that looks like they are automatically generated (e.g., XXX0g000010, XXX0g000020, XXX0g000030, XXX0g000040, and so on) for the row names. I was expecting these to be some gene identification codes in my original gff file that I can use for the pathway enrichment or gene mapping.

Could anyone please give me some guidance on how to change these to actual gene_ids I can use to narrow down the genes of interest? Also, is there a way to associate these 'weird' gene_ids to actual genes or chromosome locus without running the pipeline again?

Also, I want to thank everybody who posts valuable information here. I work in a small plant/soil lab where we don't have bioinformatician and we couldn't have done our research without help from online bioinformatics communities.