This is a test version of Biostars. For the public version, visit https://www.biostars.org.
0 votes
0 replies
143 views
Filtering scATAC seq peaks based on MACs2 scores
scatacseq macs2
written by raphael.B • raphael.B
0 votes
0 replies
178 views
Discrepancies between RAVEN getKEGGModelForOrganism and BlastKOALA KO annotations
blastkoala raven
written by sandrasn22 • sandrasn22
0 votes
0 replies
147 views
GROMACS pdb2gmx Warning: Missing Atoms (H and O) in AlphaFold3-Derived TCR–pMHC Structure
md tcr-pmhc simulations gromacs
updated by GenoMax GenoMax • written by rachana • rachana
0 votes
2 replies
681 views
alignement of human cells infected with a virus
host-virus
updated by michael.ante michael.ante • written by hajar • hajar
0 votes
0 replies
282 views
News: 2026 Genome Assembly & Annotation course - online, 9–13 March
galaxy genomeassembly genomeannotation
written by Physalia-courses Physalia-courses
0 votes
2 replies
537 views
Question Regarding Adapter Detection with fastp and Trimming with Trimmomatic
rna-se adapter fastp trimmomatic
updated by Arup Ghosh Arup Ghosh • written by mahsa80.mm • mahsa80.mm
5 votes
4 replies
1.3K views
Tool: Stop letting your AI agent hallucinate bioinformatics code — I built a 140-skill knowledge base to fix that
agent claude ai skills
updated by colindaven colindaven • written by Jaechang • Jaechang
0 votes
3 replies
1.5K views
Identifying a true viral genomic deletion, how to distinguish real deletions from quasispecies noise in IGV coverage gaps
deletion detection
updated by GenoMax GenoMax • written by tomas • tomas
0 votes
4 replies
521 views
How to get, which genes are osscilatory in nature in Euglena gracilis.
circadian rhythm
updated by Dunois • Dunois • written by ashishkumar30121999 • ashishkumar30121999
0 votes
3 replies
615 views
What file types can I use for the comparison of proteomes?
patric proteome
updated by Ram Ram • written by marongiu.luigi marongiu.luigi
0 votes
0 replies
151 views
Blog: Interval operations benchmark for Python libraries
operations python interval benchmark
written by Marek • Marek
0 votes
6 replies
4.4K views
Subset Seurat Object based on metadata
seurat
updated by Ram Ram • written by Nona • Nona
0 votes
8 replies
41K views
How to get subset of a Seurat object based on metadata?
scrna-seq seurat
updated by JackShao • JackShao • written by sunyeping • sunyeping
0 votes
0 replies
187 views
Differences between SNPs and Allele coverage for Prediction
variant genetics coverage calling
written by Loïc • Loïc
0 votes
0 replies
261 views
tbtool export svg for gene structure (exon/intron)
gene tbtool structure
written by HajiNasrollah • HajiNasrollah
0 votes
7 replies
808 views
scRNA datasets integration
scrnaseq integration batch_correction
written by mrashad mrashad
0 votes
0 replies
354 views
News: UC Davis Bioinformatics Core online workshops registration is now live for 2026!
workshop
written by najoshi • najoshi
0 votes
1 reply
349 views
Manhattan plot of Fisher's Exact Test results
manhattanplot
updated by dthorbur dthorbur • written by al • al
8 votes
4 replies
700 views
Blog: On the capabilities of modern AI coding models in developing genomics software
transcriptomics mapping algorithms ai
updated by Dunois • Dunois • written by Rob Rob
0 votes
0 replies
194 views
gff file for Circos TBTools
mcscanx tbtools circos gff
updated by Pierre Lindenbaum Pierre Lindenbaum • written by catscampos • catscampos
0 votes
4 replies
579 views
Does GATK output partial genotypes, where only one allele in a diploid individual is called
variantcalling genotyping gatk
written by Em • Em
0 votes
0 replies
167 views
WGCNA Scale Independence Problem
wgcna
written by Siobhan • Siobhan
0 votes
1 reply
369 views
PASA- annotation comparison step
rna-seq pasa genomeassembly
updated by kalavattam • kalavattam • written by rachana • rachana
1 vote
0 replies
244 views
News: Course: Modern Statistical Thinking for Biologists (Bayesian perspective)
bayes course modelling biostatistics
written by Rosina Savisaar • Rosina Savisaar
1 vote
0 replies
157 views
Tool: SquiDBase: a community resource of raw nanopore data from microbes
metadata nanopore repository
written by Arup Ghosh Arup Ghosh
0 votes
3 replies
7.8K views
Removing specific cluster based on one gene down regulation
single-cell seurat scrna-seq
updated by germansalcedo542 • germansalcedo542 • written by nitin • nitin
1 vote
7 replies
13K views
How to download triple negative breast cancer RNA-seq fpkm data from GDC.
rna-seq sequencing
updated by Lucía • Lucía • written by mtkk94 • mtkk94
0 votes
2 replies
463 views
Extracting library information from fastq file to add read group with GATK
read library illumina group gatk
updated by GenoMax GenoMax • written by Noctiluca • Noctiluca
0 votes
2 replies
576 views
Ribo-seq: Should low-quality reads be filtered at FASTQ or BAM stage after fastp trimming?
qualitycontrol riboseq trimming
written by Sammy • Sammy
0 votes
1 reply
595 views
SCTransform vs LogNormalize for preprocessing scRNA-seq data before cMonkey biclustering
single-cell seurat cmonkey
updated by Ram Ram • written by arjunp22 • arjunp22
0 votes
1 reply
313 views
News: Machine Learning for Bio-Imaging course - online, 10-12 March
machinelearning bio-imaging python deeplearning
written by Physalia-courses Physalia-courses
0 votes
2 replies
406 views
Ultima wgs quality control
ultima wgs
updated by samuel.a.odonnell samuel.a.odonnell • written by SeoG • SeoG
0 votes
0 replies
332 views
Estimating DUF1220 (Olduvai domain) copy numbers in Denisova 25 high-coverage genome (Peyrégne et al., 2025 bioRxiv)
ancient-dna duf1220 denisova 25
written by needininfo • needininfo
0 votes
0 replies
209 views
Blog: Benchmarking Genomic Format Readers in Python with Polars
python polars
written by Marek • Marek
0 votes
10 replies
2.8K views
Bioinformatics students: Air or Pro?
laptop macbook
updated by Ram Ram • written by rachana • rachana
0 votes
2 replies
418 views
polyA content in RNA-Seq samples
check rna-seq quality
updated by michael.ante michael.ante • written by pinheirofabiano • pinheirofabiano
0 votes
0 replies
205 views
News: Comparative Genomics course. - online, 23–27 February
genomeannotation snvs svs comparativegenomics
written by Physalia-courses Physalia-courses
0 votes
0 replies
204 views
News: UConn CBC - Virtual RNA-seq Workshop (Feb 24-26th)
hpc workshop r rnaseq
written by bioadam • bioadam
1 vote
0 replies
1.2K views
Python tools for gene annotation, ontology & gene set analysis
gene ontology annotation databases single-cell
updated by Ira • Ira • written by PianoEntropy • PianoEntropy
0 votes
0 replies
183 views
HIV LTR regions
hiv ngs
written by hajar • hajar
1 vote
6 replies
1.0K views
Genome assembly reference .fasta + Illumina reads
illumina assembly reference
written by A_heath • A_heath
0 votes
1 reply
529 views
ML project ideas in bioinformatics to get started
machinelearning project cancer transcriptomics genomics
updated by Pierre Lindenbaum Pierre Lindenbaum • written by rachana • rachana
0 votes
0 replies
195 views
Classifying TE-containing RNA-seq transcripts into TE-initiated, exonized, and terminated categories
genomeassembly genomeannotation transposons retrotransposons transposableelements
written by rachana • rachana
0 votes
2 replies
730 views
Best way to deal with contamination in RNA bulk seq data
rnaseq contamination bulkseq deseq2 decontamination
written by DM95 • DM95
0 votes
0 replies
295 views
Job: Postdoctoral Associate - Bioinformatics Education - Baylor College of Medicine - Houston, Texas, USA
postdoc job r
written by Erik Wright Erik Wright
0 votes
3 replies
506 views
Forum: Journals for Bioinformatic and Metagenomic Studies?
bioinformatics learning machine journal
updated by ATpoint ATpoint • written by egascon • egascon
0 votes
2 replies
1.3K views
How to remove gap-only columns from a multiple sequence alignment in FASTA with Jalview and how to edit genes? Also, how to extract genes without gaps from an alignment on Linux?
fasta alignment jalview
written by ivaldakoyo • ivaldakoyo
0 votes
2 replies
503 views
Stereoseq workflow analysis
spatial transcriptomic
written by Synat • Synat
0 votes
9 replies
1.2K views
Fastq with more reads than fast5 files
nanopore ont fast5 fastq sequencing
written by Anna • Anna
0 votes
3 replies
476 views
Transposable Elements Community Hub
genome-assembly transposable-elements genome-annotation transposons retrotransposons
updated by Ram Ram • written by rachana • rachana
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