This is a test version of Biostars. For the public version, visit https://www.biostars.org.
0 votes
1 reply
71 views
Extract gene signature from bulk rnaseq and apply to scrnaseq dataset
gene_signature bulk scrnaseq rnaseq
updated by SeqBench • SeqBench • written by asmariyaz23 • asmariyaz23
0 votes
2 replies
201 views
Tool: AI in Biology - ad for VigyanLLM
bioinformatic ai tools
updated by Aditya • Aditya • written by Hemant • Hemant
0 votes
1 reply
95 views
What are best practices for which sites to report Ti/Tv on for human WGS QC?
transition transversion
updated by SeqBench • SeqBench • written by curious curious
0 votes
2 replies
121 views
Forum: Roadmap advice for a biochemistry/biotech grad transitioning into computational cancer biology
metabolomics career-advice cancer-genomics
updated by SeqBench • SeqBench • written by ndybdaltyf6 • ndybdaltyf6
0 votes
6 replies
217 views
Alternative annotation tools for GO/KEGG enrichment
go kegg wgcna
written by CaERu _no_ korokoro • CaERu _no_ korokoro
0 votes
0 replies
49 views
Job: Postdoctoral Position at the NIEHS, NC, USA
computational-biology bioinformatics systems-biology
updated by colindaven colindaven • written by anb28636 • anb28636
1 vote
1 reply
87 views
Question about constructing a consensus peak file for diffTF
atacseq difftf diffbind
updated by SeqBench • SeqBench • written by lilithslily • lilithslily
2 votes
5 replies
182 views
fold enrichment between genomic regions/loci
statistical-test fold-enrichment variant-calling
updated by SeqBench • SeqBench • written by Matteo Ungaro • Matteo Ungaro
0 votes
1 reply
63 views
Merging of vcf data of two different variant callers and two sequencing platforms
variant_calling
updated by SeqBench • SeqBench • written by buttaasif110 • buttaasif110
0 votes
1 reply
81 views
Predicting functional impact of a rare heterozygous missense variant (p.I294T) in AJAP1: Partial vs. complete LoF?
variant-effects protein-structure
updated by Mensur Dlakic Mensur Dlakic • written by maximilian.info • maximilian.info
0 votes
3 replies
186 views
News: FINAL CALL - A Practical Introduction to NGS Data Analysis and Variant Calling (Munich, Germany | September 9–11, 2026)
variantcalling rna-seq dna-seq illumina workshop
written by ecSeq Bioinformatics • ecSeq Bioinformatics
0 votes
3 replies
131 views
DESeq2 results show the opposite log2FoldChange direction compared to the published RNA-seq study
deseq2
updated by Istvan Albert Istvan Albert • written by ashraffouad1998 • ashraffouad1998
0 votes
1 reply
96 views
How to actually identify which transcription factors are actively regulating a pathway/gene panel
algorithms transcription factor scoring
updated by kalavattam • kalavattam • written by Parth • Parth
0 votes
4 replies
128 views
Linkage prune VCF before ML phylogeny inference (e.g. IQ-TREE)?
iq-tree ld snp phylogeny wgs
written by maxrwjones • maxrwjones
1 vote
3 replies
141 views
Resources for understanding variant calling pipeline outputs
variant calling ngs
updated by Prash • Prash • written by ptalebic • ptalebic
0 votes
0 replies
35 views
News: Population Genomics workshop - online, 21–25 September
populationgenomics adna ancientdna
written by Physalia-courses Physalia-courses
0 votes
1 reply
67 views
Why were no loci realigned after bcftools normalize?
data genetic bcftools snpfiltering normalize
updated by Pierre Lindenbaum Pierre Lindenbaum • written by erika.a.dunn • erika.a.dunn
0 votes
5 replies
194 views
Issue with FASTQs of 10X Flex with Antibody Capture
scrna 10x
updated by ATpoint ATpoint • written by 10x_user • 10x_user
0 votes
0 replies
50 views
CIBERSORTx Fractions/HiRes: which mixture/signature-matrix combination is actually used internally with S-mode batch correction?
batch-effect deconvolution single-cell-rnaseq microarray cibersortx
updated by Chrs • Chrs • written by Francesco • Francesco
0 votes
5 replies
209 views
calculate the median k-mer coverage from a genomic BAM file command- linux
bam k-mer nipt
written by Ajay Narayan • Ajay Narayan
0 votes
2 replies
154 views
Detecting real vs artifact inversions in IGV
igv
updated by SeqBench • SeqBench • written by ahoerl • ahoerl
1 vote
1 reply
131 views
Relevance of strand direction in promoter motif analysis.
motif moods promoter transcription
updated by SeqBench • SeqBench • written by Shakunthala Natarajan • Shakunthala Natarajan
0 votes
1 reply
97 views
filter out low quality variants
variant illumina calling filteration
updated by Aditya • Aditya • written by a.br.ravichandran • a.br.ravichandran
0 votes
5 replies
199 views
STAR number of input reads | 0
star rnaseq
written by paxton • paxton
0 votes
2 replies
176 views
Species matching IgG controls in CUT&RUN experiment
species cut and run igg
updated by Alisa • Alisa • written by kevin.stachelek • kevin.stachelek
0 votes
1 reply
92 views
How to retrieve STRING preferredName from amino acid sequence using the STRING API?
python api preferredname string-db protein-sequence
updated by SeqBench • SeqBench • written by anadomingues • anadomingues
0 votes
3 replies
185 views
Get average quality score per position in an aligned bam file
nanopore samtools bam phred33 quality
updated by GenoMax GenoMax • written by cedric.blais • cedric.blais
0 votes
1 reply
73 views
Proper Execution of Codon Usage Bias
dnasp mega codon usage
updated by SeqBench • SeqBench • written by RCMC • RCMC
0 votes
2 replies
92 views
How can I locate the IIS6 region and the L1014F mutation in the full VGSC sequence?
primer design
updated by SeqBench • SeqBench • written by tahreem • tahreem
0 votes
3 replies
174 views
Tool: Loom - brings fragmented spatial transcriptomics workflows into one platform - need feedbacks
spatial automatic analysis integration transcriptomics
written by Olivia • Olivia
10 votes
8 replies
532 views
Forum: AI for bioinformatics pipeline development. Is it a good idea?
bioinformatics ngs pipelinedevelopment artificialintelligence
updated by zabiullama • zabiullama • written by David Langenberger David Langenberger
0 votes
0 replies
57 views
News: AI-assisted coding directly inside your R session
llms ai r agenticai
written by Physalia-courses Physalia-courses
0 votes
2 replies
228 views
Job: Interested to work
student
updated by Ajay Narayan • Ajay Narayan • written by kvruchitha02 • kvruchitha02
0 votes
6 replies
2.5K views
How long should the AAA... sequence be at the end of read, so that fastqc and multiqc consider it as poly- tail
multiqc fastqc polya
updated by GenoMax GenoMax • written by poecile.pal • poecile.pal
1 vote
4 replies
194 views
Tool: Improved prediction of microbial optimal growth temperatures
machine_learning sequence-based_predictions neural_network protein_language_models
updated by GenoMax GenoMax • written by Mensur Dlakic Mensur Dlakic
0 votes
2 replies
6.2K views
Merging FASTA files
fasta sequences
updated by pinheirofabiano • pinheirofabiano • written by l.souza l.souza
0 votes
0 replies
41 views
News: Genomic Prediction of Complex Traits | Live Online Course | Statistical Genomics & Genomic Prediction
complex traits prediction genomic gwas
updated by GenoMax GenoMax • written by coursesinfo • coursesinfo
0 votes
2 replies
168 views
Forum: Experienced bioinformatician, zero UK interviews, what am I missing?
uk jobs bioinformatics
written by adarsh • adarsh
0 votes
5 replies
226 views
Getting the mRNA data from the GEO accession number
geo number mrna accession
updated by Arup Ghosh Arup Ghosh • written by rajdeepboral00 • rajdeepboral00
0 votes
0 replies
48 views
RUVg workflow with DESeq2: covariates in first-pass design, and collinearity between W factors and known covariates
rnaseq deseq2 ruvseq
written by gallimaria657 • gallimaria657
0 votes
1 reply
97 views
Tool: My Project: RNA-seq Differential Expression Report Generator
genomics bioinformatics rnaseq transcriptomics
updated by ATpoint ATpoint • written by Penpichaya • Penpichaya
0 votes
1 reply
80 views
in silico vaccine design
vaccine insilico
updated by dthorbur dthorbur • written by lamiajerishubah • lamiajerishubah
0 votes
0 replies
53 views
News: Online course: Machine Learning for Multi-Omics Integration (21–23 September)
omicsintegration machinelearning multiomics
updated by GenoMax GenoMax • written by Physalia-courses Physalia-courses
0 votes
2 replies
192 views
Forum: Real-world adoption of AI/ML in bioinformatics workflows: Questions from a junior researcher
bioinformatics machine-learning career discussion artificial-intelligence
updated by i.sudbery i.sudbery • written by oguzhanisilay • oguzhanisilay
0 votes
1 reply
113 views
Correct way of doing enrichment analysis (ORA)
enrichment analysis transcriptomics over representation
updated by i.sudbery i.sudbery • written by carolofharvest • carolofharvest
0 votes
0 replies
31 views
Tool: hlaconcord — harmonize & cross-check HLA typing across OptiType / arcasHLA / HLA-LA / HLA-HD
software ngs hla-typing tools hla
written by Leon • Leon
0 votes
2 replies
131 views
HaplotypeCaller parameter `--ploidy-regions` regarding the PAR regions on XY chromosomes
gatk haplotypecaller par
written by Xiaokang • Xiaokang
0 votes
2 replies
141 views
Brain datasets
rnaseq neuroscience brain dataset
updated by ATpoint ATpoint • written by aj123 aj123
1 vote
2 replies
129 views
How can I conduct a secondary analysis of HLA gene genomic variation across different geographic and ethnic populations, such as American, European, South Asian, and Mongolian populations?
data genomic analysis
updated by dthorbur dthorbur • written by backupdata • backupdata
2 votes
3 replies
167 views
Can someone explain why are my Gnomad WGS AFs often 10x the Gnomad WES AF
frequencies gnomad allele
updated by Jeremy Leipzig Jeremy Leipzig • written by stuart archer • stuart archer
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