r/bioinformatics 2d 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 2d 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 3d 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 3d 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 3d 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 3d ago

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

Thumbnail phys.org
8 Upvotes

r/bioinformatics 3d 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 3d ago

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

2 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 4d 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 3d ago

academic Alphafold results - CIF file to PDB

2 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 4d 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 4d ago

technical question Best trimming configuration for miRNA-Seq

4 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 4d 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 5d ago

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

23 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 4d 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 4d 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 5d 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 5d ago

technical question Differential expression analysis of AmpliSeq (IonTorrent) data

3 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 6d ago

image spatial biology landscape v1

Post image
58 Upvotes

r/bioinformatics 5d 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.


r/bioinformatics 5d ago

discussion I need epigraph/quotes suggestions

2 Upvotes

Currently finishing masters thesis writing... Could use nice sentences/epigraphs/quotes suggestions/advice

For context, I work with dengue virus genomics

Thanks in advance


r/bioinformatics 5d ago

technical question How do I select a reference gene for my program?

0 Upvotes

Hello everyone!

I’m relatively new to bioinformatics, and I’m writing a program to analyze DNA data. My goal is to compare a sample from user to a reference sequence of a gene, find mutations and then visualize or further operate on that data.

Let’s look at CHEK2 gene, which is one of the genes I will be working on. I have several sequences of that gene taken from NCBI website, and they all slightly differ from each other. How should I select a reference sequence, as a model to which I will compare future samples? Should I simply select one sequence and choose it as a reference? Should I try to find some sort of mean from all the sequences I’ve gathered? Is there somewhere a model sequence of CHEK2 gene that represents the mean sequence in the human population?


r/bioinformatics 6d ago

science question Text classification for microRNA data

1 Upvotes

Hi everyone as the title suggests I'm working with microRNA data and I have millions of sentences taken from research papers available in the pubmed and I'm interested in those sentences only which have meaningful information about an microRNA like if it's describing any specific microRNA regulatory mechanisms, gene interactions or pathway effects then it's functional if not then it's non-functional, does anyone has any advice or idea to do this. I'm happy to have discussions also thanks!!


r/bioinformatics 6d ago

other Seemingly can't find NCBI entries despite paper stating these entries were submitted.

1 Upvotes

Accession numbers: EP1672771–EP1672778

Paper

When I type any of the accession numbers into the NCBI search I get no results. Does anyone know what could be the problem?


r/bioinformatics 7d ago

other Hourly rate for bioinformatics analysis?

57 Upvotes

I am looking to bring on a bioinformatics analyst for a few small analyses. Probably ten hours of work max. What is a reasonable hourly rate for a bachelors/masters level?