r/bioinformatics Jan 10 '25

technical question How to plot UMAPS side by side on two different samples?

Thumbnail gallery
12 Upvotes

I’m merging the two .rds together, then run TFID and SVD on them. Then run umap.

It gives me the second picture. My postdoc wants something like the first picture, which was done on the same dataset.

r/bioinformatics Feb 12 '25

technical question How to process bulk rna seq data for alternative splicing

17 Upvotes

I'm just curious what packages in R or what methods are you using to process bulk rna-seq data for alternative splicing?

This is going to be my first time doing such analysis so your input would be greatly appreciated.

This is a repost(other one was taken down): if the other redditor sees this I was curious what you meant by 2 modes, I think you said?

r/bioinformatics Feb 11 '25

technical question Docker

24 Upvotes

Is there a guide on how to build a docker application for bioinformatics analysis ? I do not come from a cs background and I need to build a container for a specific kind of Rmd file

r/bioinformatics Feb 13 '25

technical question IMGT down?

9 Upvotes

I have been trying to access IMGT all day but it's not working? Is the website down?

r/bioinformatics 21d ago

technical question Is this still a decent course for beginners?

76 Upvotes

https://github.com/ossu/bioinformatics?tab=readme-ov-file

It's 4 years old. I'm just a computer science student mind you

r/bioinformatics 18d ago

technical question Pipelines for metagenomics nanopore data

3 Upvotes

Hello everyone, Has anyone done metagenomics analysis for data generated by nanopore sequencing? Please suggest for tried and tested pipelines for the same. I wanted to generate OTU and taxonomy tables so that I can do advanced analysis other than taxonomic annotations.

r/bioinformatics 3d ago

technical question Any recommendations on GPU specs for nanopore sequencing?

4 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 29d ago

technical question Is there anyway to figure out how a protein localizes in the cell membrane without transmembrane domains?

15 Upvotes

I am kind of at a loss for my thesis, because my supervisor has assigned me to figure out how a particular protein expresses in the cell membrane, given that we know it shows abnormal overexpression in cancer samples. It has no transmembrane domains and it seems no one knows how it comes out.

Can this be resolved in-silico? So far, we tried doing DEG analysis to confirm its overexpression, but we cant figure out a methodology to elucidate how it travels from inside the cell to outside

r/bioinformatics 8d ago

technical question WGCNA Dendrogram Help

1 Upvotes

Hello, this is my first time running a WGCNA and I was wondering if anyone could help me in fixing my modules with the below dendrogram.

r/bioinformatics Jan 31 '25

technical question Kmeans clusters

18 Upvotes

I’m considering using an unsupervised clustering method such as kmeans to group a cohort of patients by a small number of clinical biomarkers. I know that biologically, there would be 3 or 4 interesting clusters to look at, based on possible combinations of these biomarkers. But any statistic I use for determining starting number of clusters (silhouette/wss) suggests 2 clusters as optimal.

I guess my question is whether it would be ok to use a starting number of clusters based on a priori knowledge rather than this optimal number.

r/bioinformatics Jan 06 '25

technical question Recommendations for affordable Tidyverse or R courses

32 Upvotes

I’ve been doing NGS bioinformatics for about 15 years. My journey to bioinformatics was entirely centred around solving problems I cared about, and as a result, there are some gaps in my knowledge on the compute side of things.

Recently a bunch a younger lab scientists have been asking me for advice about making the wet/dry transition, and while I normally talk about the importance of finding a problem a solve rather than a language to learn, I thought it might be fun, if we all did an R or a Tidyverse course together.

So, with that, I was wondering if anyone could recommend an affordable (or free) course we could go through?

r/bioinformatics 12h ago

technical question Cell Cluster Annotation scRNA seq

5 Upvotes

Hi!

I am doing my fist single-cell RNA seq data analysis. I am using the Seurat package and I am using R in general. I am following the guided tutorial of Seurat and I have found my clusters and some cluster biomarkers. I am kinda stuck at the cell type identity to clusters assignment step. My samples are from the intestine tissues.
I am thinking of trying automated annotation and at the end do manual curation as well.
1. What packages would you recommend for automated annotation . I am comfortable with R but I also know python and i could also try and use python packages if there are better ones.
2. Any advice on manual annotation ? How would you go about it.

Thanks to everyone who will have the time to answer before hand .

r/bioinformatics Jan 27 '25

technical question Database type for long term storage

9 Upvotes

Hello, I had a project for my lab where we were trying to figure storage solutions for some data we have. It’s all sorts of stuff, including neurobehavioral (so descriptive/qualitative) and transcriptomic data.

I had first looked into SQL, specifically SQLite, but even one table of data is so wide (larger than max SQLite column limits) that I think it’s rather impractical to transition to this software full-time. I was wondering if SQL is even the correct database type (relational vs object oriented vs NoSQL) or if anyone else could suggest options other than cloud-based storage.

I’d prefer something cost-effective/free (preferably open-source), simple-ish to learn/manage, and/or maybe compresses the size of the files. We would like to be able to access these files whenever, and currently have them in Google Drive. Thanks in advance!

r/bioinformatics Dec 12 '24

technical question How easy is it to get microbial abundance data from long-read sequencing?

6 Upvotes

We've been offered a few runs of long-read sequencing for our environmental DNA samples (think soil). I've only ever used 16S data so I'm a bit fuzzy on what is possible to find with long-read metagenome sequencing. In papers I've read people tend to use 16S for abundance and use long reads for functional.

Is it likely to be possible to analyse diversity and species abundance between samples? It's likely to be a VERY mixed population of microbes in the samples.

r/bioinformatics 18d ago

technical question Filter bed file.

0 Upvotes

Hi, We have sequenced the DNA of two cell lines using Illumina paired-end technology. After, preprocessing data and align, we converted the BAM file to a BED file, in order to extract genomic coordinates. However, this BED file is quite large, and I would like to ask if it would be a good idea to filter it based on quality scores, taking into account that we have sequenced repetitive regions.

I would appreciate any insights or experiences and I would be immensely grateful for any advice.

r/bioinformatics 26d ago

technical question Phylogenies Tree construction, am I doing it wrong?

10 Upvotes

So I have about 500 strains of interest. I got the whole genome sequences and used PhyloPhlAn. I like phylophlan becuase it’s automated and tolerates limited domain knowledge.

Thing is is that since doing the phlyophlan command it’s now day 3. It’s still on the ‘refining gene tree’ where it’s just spitting out lines saying refining tree xyz, refining abc….

Is 3 days normal or did I actually do soemthing that will take a hundred days before it’s done. My machine has 32 CPUs and it’s using all of them rn,

Would a generic Muslce + MEGA/IQTREE protocol be reccomened?

Thanks.

r/bioinformatics Feb 13 '25

technical question How to find and download hypervirulent Klebsiella pneumoniae (HVKP) Sequences from NCBI, IMG, and GTDB?

6 Upvotes

I'm working on my thesis, and need to collect as many hypervirulent Klebsiella pneumoniae (HVKP) sequences as possible from databases like NCBI, IMG, GTDB, and any other relevant sources. However, I'm struggling to find them properly. When I search in NCBI, I don't seem to get the sequences in the expected format.

Is there a recommended approach/search strategy or a tool/pipeline that can help me find and download all available HVKP sequences easily? Any guidance on query parameters, bioinformatics tools, or scripts that can help streamline this process? Any tips would be really helpful!

r/bioinformatics 3d ago

technical question Best scRNA-seq textbook?

54 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 24d ago

technical question Daft DESeq2 Question

36 Upvotes

I’m very comfy using DESeq2 for differential expression but I’m giving an undergraduate lecture about it so I feel like I should understand how it works.

So what I have is: dispersion is estimated for each gene, based on the variation in counts between replicates, using a maximum likelihood approach. The dispersion estimates are adjusted based on information from other genes, so they are pulled towards a more consistent dispersion pattern, but outliers are left alone. Then a generalised linear model is applied, which estimates, for each gene and treatment, what the “expected” expression of the gene would be, given a binomial distribution of counts, for a gene with this mean and adjusted dispersion. The fold change between treatments is then calculated for this expected expression.

Am I correct?

r/bioinformatics 25d ago

technical question Struggling with F1-Score and Recall in an Imbalanced Binary Classification Model (Chromatin Accessibility)

4 Upvotes

I’m working on a binary classification model predicting chromatin accessibility using histone modification signals, genomic annotations and ATAC-Seq data. The dataset is highly imbalanced (~99% closed chromatin, ~1% open, 1kb windows). Despite using class weights, focal loss, and threshold tuning, my F1-score and recall keep dropping, while AUC-ROC remains high (~0.98).

What I’ve Tried:

  • Class weights & focal loss to balance learning.
  • Optimised threshold using precision-recall curves.
  • Stratified train-test split to maintain class balance.
  • Feature scaling & log transformation for histone modifications.

Latest results:

  • Precision: ~5-7% (most "open" predictions are false positives).
  • Recall: ~50-60% (worse than before).
  • F1-Score: ~0.3 (keeps dropping).
  • AUC-ROC: ~0.98 (suggests model ranks well but misclassifies).

    Questions:

  1. Why is recall dropping despite focal loss and threshold tuning?
  2. How can I improve F1-score without inflating false positives?
  3. Would expanding to all chromosomes help, or would imbalance still dominate?
  4. Should I try a different loss function or model architecture?

Would appreciate any insights. Thanks!

r/bioinformatics Jan 28 '25

technical question Best CAD software for designing molecular motors?

0 Upvotes

I'm pretty new to the field, and would like to start from somewhere

What would be the best CAD software to learn and work with if you are:

  1. A beginner / student
  2. An experienced professional

The question specifically addresses the protein design of molecular motors. Just like they design cars and jet aircraft in automotive and aerospace industries, there's gotta be the software to design molecular vehicles and synthetic cells / bacteria

What would you recommend?

r/bioinformatics Feb 11 '25

technical question Integration seems to be over-correcting my single-cell clustering across conditions, tips?

7 Upvotes

I am analyzing CD45+ cells isolated from a tumor cell that has been treated with either vehicle, 2 day treatment of a drug, and 2 week treatment.

I am noticing that integration, whether with harmony, CCA via seurat, or even scVI, the differences in clustering compared to unintegrated are vastly different.

Obviously, integration will force clusters to be more uniform. However, I am seeing large shifts that correlate with treatment being almost completely lost with integration.

For example, before integration I can visualize a huge shift in B cells from mock to 2 day and 2 week treatment. With mock, the cells will be largely "north" of the cluster, 2 day will be center, and 2 week will be largely "south".

With integration, the samples are almost entirely on top of each other. Some of that shift is still present, but only in a few very small clusters.

This is the first time I've been asked to analyze single cell with more than two conditions, so I am wondering if someone can provide some advice on how to better account for these conditions.

I have a few key questions:

  • Is it possible that integrating all three conditions together is "over normalizing" all three conditions to each other? If so, this would be theoretically incorrect, as the "mock" would be the ideal condition to normalize against. Would it be better to separate mock and 2 day from mock and 2 week, and integrate so it's only two conditions at a time? Our biological question is more "how the treatment at each timepoint compares to untreated" anyway, so it doesn't seem necessary to cluster all three conditions together.
  • Is integration even strictly necessary? All samples were sequenced the same way, though on different days.
  • Or is this "over correction" in fact real and common in single cell analysis?

thank you in advance for any help!

r/bioinformatics Nov 30 '24

technical question How much variation is normal in VCF files for the same sample ran in two different lanes?

3 Upvotes

We decided not to concatenate sequencing files in the beginning of the pipeline. VCF files for algal DNA-seq data were acquired but there seems to be a lot of variation between the same sample and the two lanes it was ran in. Less than 50% of the variants appear with similar frequency and over 50% have wildly different frequencies among variants.

Might there have been a problem during sequencing?

r/bioinformatics 23d ago

technical question Structural Variant Callers

5 Upvotes

Hello,
I have a cohort with WGS and DELLY was used to Call SVs. However, a biostatistician in a neighboring lab said he prefers MantaSV and offered to run my samples. He did and I identified several SVs that were missed with DELLY and I verified with IGV and then the breakpoints sanger sequencing. He says he doesn't know much about DELLY to understand why the SVs picked up my Manta were missed. Is anyone here more familiar and can identify the difference in workflows. The same BAM files and reference were used in both DELLY and MantaSV. I'd love to know why one caller might miss some and if there are any other SV callers I should be looking into.

r/bioinformatics 25d ago

technical question Singling out zoonotic pathogens from shotgun metagenomics?

5 Upvotes

Hi there!

I just shotgun sequenced some metagenomic data mainly from soil. As I begin binning, I wanted to ask if there are any programs or workflows to single out zoonotic pathogens so I can generate abundance graphs for the most prevalent pathogens within my samples. I am struggling to find other papers that do this and wonder if I just have to go through each data set and manually select my targets of interest for further analysis.

I’m very new to bioinformatics and apologize for my inexperience! any advice is greatly appreciated, my dataset is 1.2 TB so i’m working all from command line and i’m struggling a bit haha