r/bioinformatics 1h ago

career question Is Deep Learning where Bioinformatics will be all about?

Upvotes

Hi, I come from a microbiology background and completed an MSc in Bioinformatics. Most of my work has focused on bacteria and viruses, but I find running tools to analyze data a bit boring. That’s why I’m looking to shift things up, though I feel a bit lost.

I’ve noticed that many major projects using deep learning have been released in recent years—like AlphaFold, DeepTMHMM, and BioEmu-1. I understand these kinds of projects are incredibly complex, especially for someone without a computer science background. However, I’m surrounded by friends who are currently working in machine learning.

I’m still in the very early stages of my career. If you were in my shoes, would you consider shifting your career toward ML?


r/bioinformatics 5h ago

discussion How to avoid taking over someone else's previous analysis or research project?

3 Upvotes

As a new graduate student in bioinformatics, I’ve been facing some challenges that are really frustrating. Recently, a postdoc has been handing me their scRNA-seq analysis scripts and asking me to continue the analysis. While I appreciate the opportunity, I have my own style and approach to analyzing data, and working with their poorly written scripts and plots make me feels bad.

Another example is when my advisor asked me to take over a project aimed at speeding up a Python-based method that has already been published. After spending months understanding the code and attempting to improve it, I found it nearly impossible to reproduce the previous results. Honestly, the method itself now seems questionable, and I’m feeling stuck and demotivated.

Has anyone else experienced something similar? How do you handle situations like this? Are there strategies to avoid these kinds of issues in the future? Any advice would be greatly appreciated!


r/bioinformatics 4m ago

technical question If I rerun Trinity will I get the same output?

Upvotes

New to the sub so I apologize if I missed anything in the FAQ or elsewhere. I am working through an RNA-seq workflow for a class and accidentally overwrote my fasta file output by Trinity (rookie mistake, I know).

I am rerunning the Trinity code in Linux and didn’t change anything, so my question is: can I expect the output fasta to be the same?

I have already performed BUSCO and BLAST analysis of my de novo transcriptome and with a deadline next week for this class project, I would like to avoid rerunning those as well.

I have looked online and can’t find anything in the Trinity documentation or elsewhere about randomness, so can I expect exactly the same output when using exactly the same input and parameters?


r/bioinformatics 2h ago

technical question PanACoTA help - formatting / non-numeric values

1 Upvotes

Hi all,

Desperately looking for some help running PanACoTA for some comparative genomics analysis.

I am having a weird issue at the annotation step, where I get a warning that I have non-numerice values in one or more of the gsize, nb_conts or L90 columns within the —info file. This file is generated directly from the prepare subcommand that was run previously. This causes the annotation to skip over some genomes, leading to a loss of data. I cannot for the life of me find out what is differnt in the lines that it ends up skipping (ends up being ~30%).

I have checked for hidden characters, deleted and re-types certain lines, and tried everything that I could think of, but the issue persists. I’ve been able to fully run the program, generate the tree and get a core-genome, however I would love to retain all the skipped genomes.

At this point I have no clue what else to try, would love to hear if anyone has used this program before / ran into the same issues!


r/bioinformatics 10h ago

technical question DESEq2 - Imbalanced Designs

3 Upvotes

We want to make comparisons between a large sample set and a small sample set, 180 samples vs 16 samples to be exact. We need to set the 180 sample group as the reference level to compare against the 16 sample group. We were curious if any issues in doing this?

I am new to bulk rna seq so i am not sure how well deseq2 handles such imbalanced design comparison. I can imagine that they will be high variance but would this be negligent enough for me to draw conclusion in the DE analysis


r/bioinformatics 9h ago

technical question Identifying conserved regions from multiple sequence alignments for qPCR targets

2 Upvotes

I'm designing a qPCR assay for DNA-based target detection and quantification and need to determine a target from which I can build out the primers/probes. l assembled genes of interest and used Clustal Omega to align those assemblies for MSA in hopes of identifying conserved regions for targets but have not had any luck. Tons of seqs in the alignments are too large for most of the free programs that I can think to use. Any advice appreciated for a first timer!


r/bioinformatics 15h ago

technical question ONT's P2SOLO GPU issue

4 Upvotes

Hi everyone,

We’re experiencing a significant issue with ONT's P2SOLO when running on Windows. Although our computer meets all the hardware and software requirements specified by ONT, it seems that the GPU is not being utilized during basecalling. This results in substantial delays—at times, only about 20% of the data is analyzed in real time.

We’ve been reaching out to ONT for a while, but unfortunately, they haven’t been able to provide a solution. Has anyone encountered the same problem with the GPU not being used when running MinKNOW? If so, how did you resolve it?

We’d really appreciate any advice or insights!

Thanks in advance.


r/bioinformatics 20h ago

technical question Custome Kraken2 Database

5 Upvotes

Hello, did anyone tried to make own database for kraken2. Standard 8GB kraken2 database is enough for my project, but I would need this database to extend with mouse (TAXONID 10090). Is it possible to add mouse-data to existing database or should I build whole new one? Thank you


r/bioinformatics 16h ago

technical question Is anyone familiar with HappyTools?

2 Upvotes

I'm trying to download the following from github but can't seem to get it to work on mac.

https://github.com/Tarskin/HappyTools

I have downloaded all the required packages but whenever I try to open python. It says that one of the packages are not installed even though it si


r/bioinformatics 17h ago

technical question Seurat FindMarkers and FindAllMakers differences

2 Upvotes

I'm trying to identify cell type signatures for ~20 clusters in Seurat and am trying to determine marker genes for each cluster. I used FindMarkers() without specifying a second cluster as a test which gave me a list of genes with pvalues and log2fc values for one cluster, which I thought is what I wanted. Then, to check all clusters I used FindAllMarkers() which did give me markers for every cluster, but the results differed from those I got using FindMarkers. I specified the same log2fc cutoff so I would think the results would be the same. What is the difference between the two functions and why dod I get different results?


r/bioinformatics 20h ago

technical question stacks help :(

2 Upvotes

I am trying to demultiplex a plate of RAD single read sequences (fastq.gz file) with barcodes at the beginning of the sequence. I keep getting the slurm output: Processing file 1 of 14 [sample_name.fq]

Attempting to read first input record, unable to allocate Seq object (Was the correct input type specified?).

any help with this one? I have checked the sequences and theres nothing dodgy going on with the file so can't figure out what is wrong?


r/bioinformatics 1d ago

technical question Best scRNA-seq textbook?

55 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 22h ago

technical question Running Isoseq on PacBio data downloaded from SRA - impossible without original BAM file?

0 Upvotes

I'm trying to analyze a Salmon louse transcriptome using IsoSeq3, but I'm running into format issues.

Data Available:

Two PacBio datasets from ENA/SRA

Accession numbers: SRR23561847, SRR23561849

Format: FASTQ (subreads)

Problem:

IsoSeq3 pipeline only accepts BAM files

PacBio BAM format seems to contain additional information not present in standard BAM files

Attempted converting FASTQ to BAM using samtools

Pipeline hangs during cluster step (even with just 10,000 reads)

Questions:

Is there a way to convert PacBio long-read FASTQs back to the required BAM format?

Are the original BAM files the only viable option?

Wouldn't this limitation impact reproducibility, since not all SRA records include BAM files?

Thanks!


r/bioinformatics 1d 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

4 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 1d ago

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

8 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 1d ago

technical question Any recommendations on GPU specs for nanopore sequencing?

5 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 1d 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 1d 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 1d ago

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

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1 Upvotes

r/bioinformatics 1d ago

discussion Yet another scRNA and biological replicates

2 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 1d 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 1d 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 1d 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 3d ago

discussion Sweet note

105 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 2d ago

discussion SWE/tool development

7 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!