This is a test version of Biostars. For the public version, visit https://www.biostars.org.
0 votes
0 replies
14 views
WGCNA: Should seed tissues be included with root and shoot samples when studying nitrate uptake in maize?
rnaseq wgcna plant biology transcriptomics co-expression
written by mugwimbi • mugwimbi
0 votes
1 reply
47 views
Tool: I built a browser-based toolkit for common bioinformatics and molecular biology tasks - looking for feedback
molecular-biology bioinformatics software sequence-analysis web-tools
updated by Michael Dondrup Michael Dondrup • written by Ravi • Ravi
0 votes
1 reply
53 views
News: Registration closing soon: 2nd Berlin Winter School in RNA-Seq Data Analysis, November 2–5, 2026
rnaseq transcriptomics workshop
written by ecSeq Bioinformatics • ecSeq Bioinformatics
0 votes
0 replies
22 views
PAML codeml fails with exit status 1
paml dnds phylogenomics
written by Md Hasibul • Md Hasibul
624 votes
174 replies
232K views
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated by Biostar Biostar • written by Istvan Albert Istvan Albert
1 vote
1 reply
845 views
Job: Applications Now Open – Summer 2026 Teaching Opportunities [SSPI]
temporary stem summer jobs paid
updated by Henry • Henry • written by Emaly • Emaly
0 votes
5 replies
8.1K views
bcftools mpileup --max depth : What would be a reasonable setting for this option?
bcftools mpileup consensus
updated by pnrmm • pnrmm • written by VBer VBer
0 votes
1 reply
36 views
Tool: ExomeFlow: reproducible WES analysis from paired FASTQs to annotated variants
bioinformatics
updated by Pierre Lindenbaum Pierre Lindenbaum • written by Robin • Robin
0 votes
1 reply
30 views
Tool: ATGCFLOW: web-based FASTQ-to-variant workflow with annotation and review - feedback requested
bioinformatics
updated by Pierre Lindenbaum Pierre Lindenbaum • written by Robin • Robin
0 votes
0 replies
25 views
Job: Assistant Professor in Computational and Experimental Molecular Biology
molecular-biology professor faculty
written by UCSDBioSci • UCSDBioSci
2 votes
3 replies
62 views
Difficulty separating cell types in Parse Biosciences scRNA-seq data compared with 10x Genomics
scrna-seq transcriptome parsebiosciences
updated by ATpoint ATpoint • written by Nitin Narwade Nitin Narwade
0 votes
1 reply
58 views
How to set a cutoff TPM value to determine whether a gene is expressed or not?
value tpm expression gene
updated by ATpoint ATpoint • written by Muhammad Tahmid • Muhammad Tahmid
0 votes
1 reply
58 views
Looking someone experienced in genomics/bioinformatics to help guide me through applying AlphaGenome
bioinformatics
written by entrepreneurshipa • entrepreneurshipa
0 votes
0 replies
39 views
Forum: Career advice
jobs advice bioinfo career
written by BionfoDevot • BionfoDevot
0 votes
2 replies
49 views
Molecular Loop ONT Demultiplexing
demultiplexing molecular ont loop
written by Tillie • Tillie
6 votes
3 replies
73 views
Tool: GenomeSieve: a graphical tool for filtering and downloading NCBI genome assemblies
genome ncbi software bioinformatics
updated by jpcastrodarocha • jpcastrodarocha • written by davimcampos09 • davimcampos09
1 vote
7 replies
8.3K views
Merge vcf files of structural variants
structural_variants vcf merge
updated by Qingxiang • Qingxiang • written by ma17 • ma17
0 votes
2 replies
848 views
Problem in merging multiple samples VCF file obtained from Structural variant caller Lumpy
sv variant-calling vcf
updated by GenoMax GenoMax • written by sardana.thakur.prachi • sardana.thakur.prachi
0 votes
0 replies
33 views
WGCNA removing mitochondria and ribosomal genes
wgcna
written by María José • María José
4 votes
6 replies
2.9K views
Is there any gene nomenclature conversion tool that recognizes old names?
genomics r annotation
updated by GenoMax GenoMax • written by emibaffo • emibaffo
0 votes
1 reply
40 views
Creating a custom reference with cellranger mkref for EBV B95-8: duplicate gene id
gtf cellranger mkref
updated by marco.barr • marco.barr • written by malcapi • malcapi
0 votes
0 replies
30 views
News: COURSE: AI for Drug Discovery – Machine Learning, Deep Learning and Graph Neural Networks | 12–15 October
deeplearning ai cnns machinelearning drugdiscovery
written by Physalia-courses Physalia-courses
0 votes
1 reply
70 views
Forum: Looking to gain any experience
student
updated by Arup Ghosh Arup Ghosh • written by Tafadzwa • Tafadzwa
2 votes
4 replies
119 views
exogenous gene in scRNA-sequencing
rna sequencing
updated by GenoMax GenoMax • written by Morris_Chair Morris_Chair
0 votes
0 replies
43 views
News: Workshop:Virtual Genome Assembly, Sept. 22-24, 2026
virtual genomeassembly uconn workshop
written by zsc25001 • zsc25001
2 votes
0 replies
47 views
Tool: SwiftCNV — a python tool to infer copy number variations (CNVs) from single-cell RNA-seq data
scrna cnv infercnv python
written by adrianparrilla • adrianparrilla
1 vote
3 replies
139 views
Tool: GATES: automated whole-exome sequencing analysis for somatic and germline variant discovery
germline pathogenic somatic exome variant
updated by Cyriac Kandoth Cyriac Kandoth • written by Nicholas • Nicholas
1 vote
0 replies
67 views
News: Teaching bioinformatics differently: Applied Bioinformatics 2026
bioinformatics
written by Istvan Albert Istvan Albert
0 votes
3 replies
84 views
ClusterProfiler-enrichGO questions about the universe
enrichgo clusterprofiler
updated by jared.andrews07 jared.andrews07 • written by Esperanza • Esperanza
2 votes
1 reply
81 views
Struggling to detect known partial deletion in NOTCH2 from WES (germline, small cohort, no reference panel) - CNV callers give inconsistent/wrong results
wesanalysis detectionofpartialdeletion
updated by Chris Miller Chris Miller • written by odi • odi
0 votes
0 replies
47 views
News: Online live course - Agentic AI for Life Sciences - 3-4 December
agenticai genomics ai
written by Physalia-courses Physalia-courses
0 votes
1 reply
64 views
Best practice for downstream processing of pig gene identifiers and human orthologues
analysis scrna pigs ensembl. sequencing
updated by mark.ziemann mark.ziemann • written by Arindam • Arindam
1 vote
3 replies
196 views
whole-genome sequencing of a non-model organism: from raw reads to genome assembly and gene annotation
genomic sequencing
updated by shelkmike shelkmike • written by WUSCHEL WUSCHEL
0 votes
0 replies
37 views
Question about vg giraffe haplotype sampling to genotype SVs in many samples
sv giraffe vg haplotype-sampling
updated by GenoMax GenoMax • written by Alex Samano • Alex Samano
0 votes
2 replies
81 views
Merging similar coordinates in Methylation data
methylation
written by 1769mkc 1769mkc
0 votes
4 replies
161 views
all samples are aligned vertically on the PCA
pca rna-seq
updated by ATpoint ATpoint • written by marieke • marieke
0 votes
4 replies
167 views
Biopython Entrez.efetch returning empty FASTA file when fetching NCBI nucleotide sequences
fasta biopython entrez python ncbi
written by Suriya • Suriya
0 votes
2 replies
142 views
scRNA-seq: does my DESeq2 and GSEA workflow make sense?
scrnaseq
updated by rfran010 • rfran010 • written by juliya.k • juliya.k
0 votes
0 replies
53 views
Quality control benchmark for Sanger files
control quality sanger
written by Jean • Jean
2 votes
0 replies
72 views
News: AlphaGenome Atlas: A predictive map of every possible DNA letter change in the human genome
alphagenome google
written by Pierre Lindenbaum Pierre Lindenbaum
2 votes
3 replies
225 views
News: is Biomart dead ? "We have frozen BioMart but it remains accessible via our archive servers."
ensembl
updated by Istvan Albert Istvan Albert • written by Pierre Lindenbaum Pierre Lindenbaum
0 votes
2 replies
969 views
Understanding sctransform
sctransform seurat
updated by Phi • Phi • written by Deepak Tanwar Deepak Tanwar
0 votes
1 reply
90 views
Many GEO CTCF ChIP-seq datasets have no controls: is there a different standard for CTCF ChIP-seq?
background controls chip-seq input ctcf
written by kalavattam • kalavattam
0 votes
0 replies
49 views
News: Online Course: Nextflow for Beginners – 9–11 November
reproducibility workflowmanager nextflow
written by Physalia-courses Physalia-courses
0 votes
2 replies
150 views
is this DE analysis with edgeR correct?
edger transcriptomics help
updated by Gordon Smyth Gordon Smyth • written by Estefania Belen • Estefania Belen
0 votes
0 replies
43 views
How to get permutations or derivatives of a candidate molecule?
bioinformatics screening drug chemiinformatics
written by mark.ziemann mark.ziemann
0 votes
1 reply
99 views
Forum: CHANGING CAREER: FROM EDUCATION TO BIOINFOMATICS FIELD
biostars
updated by ATpoint ATpoint • written by Ngofira • Ngofira
35 votes
36 replies
18K views
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
updated by ashish • ashish • written by Ram Ram
0 votes
0 replies
41 views
Consultation: Multisample copyKAT visualization
bioinformatic methods analysis
written by 2795906776 • 2795906776
0 votes
2 replies
125 views
Tool: spades-rs — a Rust port of SPAdes genome assembler (seeking feedback and benchmarking)
genome-assembly assembly ngs spades
written by Sagnik • Sagnik
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