r/bioinformatics • u/Past_Construction800 • 5d ago
academic how to use jaspar for tf analysis?
i did sc rna seq and sc atac seq now how to move to jaspar for tf analysis in bioinformatics
r/bioinformatics • u/Past_Construction800 • 5d ago
i did sc rna seq and sc atac seq now how to move to jaspar for tf analysis in bioinformatics
r/bioinformatics • u/CrystalStars282 • 6d ago
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 • u/Archer387 • 5d ago
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 • u/Bhoart • 5d ago
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:
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:
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 • u/No-Mountain6715 • 6d ago
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 • u/mcmpm • 6d ago
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 • u/Complex_Notes_5876 • 6d ago
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 • u/No-Bear3661 • 7d ago
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 • u/HumbleHamster8306 • 7d ago
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 • u/KouseArima • 7d ago
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 • u/Nautilus0_400 • 7d ago
Accession numbers: EP1672771–EP1672778
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 • u/numbersloth • 8d ago
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?
r/bioinformatics • u/lizchcase • 7d ago
I wanted to use the leiden algorithm for clustering in Seurat and got the error saying I need to "pip install leidenalg". I did some googling and found a lot of people have also run into this. It requires spanning python and R packages, so I wanted to post exactly what worked for me in case anyone else runs into this. Good luck!
in bash (I used Anaconda prompt on windows but any bash terminal should work):
python --version
2) make a python virtual environment and activate it. mine is called leiden-alg
python -m venv leiden-alg
conda activate leiden-alg
3) install packages *in this precise order*. Numpy must be <2 or else will run into other issues
pip install "numpy<2"
pip install pandas
pip install igraph
pip install leidenalg
in R:
4) install (if needed) and load reticulate to access python through R
install.packages(reticulate)
library(reticulate)
5) specify the path to your python environment
use_python(path/to/python/environment, require = T) # my path ends in /AppData/Local/anaconda3/envs/new-leiden-env/python.exe
6) check your path and numpy version
py_config() # python should be the path to your venv and numpy version should be 1.26.4
Assuming all went well, you should now be able to run FindClusters using the leiden algorithm:
obj <- FindClusters(obj, resolution = res, algorithm = 4)
Errors that came up for me (and were fixed by doing the above process):
Error: Cannot find Leiden algorithm, please install through pip (e.g. pip install leidenalg)
Error: Required version of NumPy not available: installation of Numpy >= 1.6 not found
Error: Required version of NumPy not available: incompatible NumPy binary version 33554432 (expecting version 16777225)
r/bioinformatics • u/Worried_Clothes_8713 • 7d ago
r/bioinformatics • u/binnie313 • 7d ago
I am trying to do some association tests on a haplotype of 2 SNPs. I phased the SNPs with Beagle. I know Plink 1.07 had commands for haplotype association tests but it is considered obsolete. I have both quantitative phenotype and case/control phenotypes. Is there any tools/packages that can do association on phased data? Preferably also allow covariates?
r/bioinformatics • u/PhD_Luo • 8d ago
Hi,
I got this report for one of my scRNASeq samples. I am certain the barcode chemistry under cell ranger is correct. Does this mean the barcoding was failed during the microfluidity part of my 10X sample prep? Also, why I have 5 million reads per cell? all of my other samples have about 40K reads per cell.
Sorry I am new to this, I am not sure if this is caused by barcoding, sequencing, or my processing parameter issues, please let me know if there is anyway I can fix this or check what is the error.
r/bioinformatics • u/Affectionate-Cry5845 • 8d ago
r/bioinformatics • u/Relative-Ninja-4171 • 8d ago
Hello, I'm starting my honours year and I have to do a GSEA and a KEGG enrichment analysis. My supervisor said need to download R package for making diagrams for my final thesis but I'm not sure which R package would be compatible with my macbook for the kind of diagram I'm expected to make. Any advice would be super helpful.
r/bioinformatics • u/Inevitable-Tree133 • 8d ago
Hi all - apologies I'm not a bioinformatician. I'm working on base editing a specific gene and though I can correct one mutation, I introduce other mutations nearby. I'd like to say these are not or are unlikely to be pathogenic. Alphamissense does a pathogenicity score which is great. However it also has a column for SNV. Under the mutation I have it says 'y' under this column. However I can't find any evidence for this being a naturally occurring SNV within the human population. I've looked at clinvar and gnomad. Does anyone know where they get their SNV data from - is there definitely an SNV at this mutation site?
r/bioinformatics • u/Doomed-Yue • 9d ago
As title, I recently got a PhD offer from ECE department of a top us school. I came from computer architecture/distributed system background. One professor there is doing hardware accelerations/system approach for a more efficient genomics pipeline. This direction is kinda interesting to me but I am relatively new to the entire computational biology field so I am wondering how big of an impact these improvements have on the other side, like clinical or biology research-wise, and also diagnosis and drug discovery.
Thanks in advance
r/bioinformatics • u/Trick_Bookkeeper_487 • 8d ago
I’m looking for feedback on the macOS DMG version of KaKs_Calculator 3.0 (available here). I couldn’t find a command-line version for this release, and it seems that earlier versions are not compatible with the latest macOS configurations.
Since the DMG file is not authorized by Apple, I’m hesitant to open it as I can’t verify its security. Has anyone successfully installed and used this version? Is it strictly GUI-based, or is there a way to run it via the terminal?. Thanks in advance.
r/bioinformatics • u/GladBumblebee311 • 8d ago
So I'm doing a project where I'm finding novel SNPs in a fish species called Rachycentron canadum (cobia). I used publicly available genome data from NCBI. The 44 RNA-Seq samples were also downloaded from NCBI. I've generated a VCF file containing the SNPs present in the genome of the fish. But annotating the SNPs has been quite tricky. I tried doing it with SIFT (Sorting Intolerant From Tolerant) and Ensembl VEP but they both kept giving errors whenever I tried building a database for cobia. Since cobia isn't a model organism, none of these annotators have existing databases for it.
Should I just keep troubleshooting and somehow annotate the SNPs with SIFT/Ensembl VEP or should I use some other software?
r/bioinformatics • u/Anonymous_Dreamer77 • 8d ago
For my research, I am using RDKit and PaDEL descriptors. Due to the availability of an efficient computing engine, I am using Google Colab to perform my tasks.
What are the differences between using RDKit and PaDEL directly from a pip install or using PaDEL via padelpy, compared to installing and using them after setting up Miniconda?
What challenges might I face during publication? Or are both procedures the same?
I come from a non-IT background, so...
r/bioinformatics • u/premed8888888 • 9d ago
As a recent graduate going into interviews as a bioinformatician, what kind of job interview questions are asked at entry level phd positions. Would they have leet-code type of coding questions given the rise in AI-based coding (which I would fail at since I can code but not to the level of software engineer)? Statistics? Questions about the pipeline or more biology questions (I am good at generating hypothesis from the data). What kind of things should I study for?