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0 votes
5 replies
1.8K views
Forum: Collaboration for phd thesis
next-gen
updated by Medhat Medhat • written by Hope AKKARI • Hope AKKARI
0 votes
0 replies
81 views
Assessing mapping quality
quality-check bcf mapping vcf
written by Noctiluca • Noctiluca
2 votes
0 replies
82 views
Why does quantile transform with uniform output outperform normal output in a deep survival model (C‑index)?
preprocessing omics quantilenormalization normalization deeplearning
written by Yugan Gogul Muthukumar • Yugan Gogul Muthukumar
0 votes
1 reply
223 views
Which allele to use as effect allele for polygenic scores?
effect pgs gwas
updated by LauferVA LauferVA • written by _quantum_girl_ • _quantum_girl_
0 votes
2 replies
199 views
Where can I find mouse BAM files?
cnv grcm39 genome mouse mm39
updated by Matthias Zepper Matthias Zepper • written by Pipschroma • Pipschroma
0 votes
2 replies
266 views
Alignment
s2 alignment extract
updated by GenoMax GenoMax • written by Ra • Ra
0 votes
4 replies
656 views
ascp suddenly fails with failed to authenticate – worked before with same setup
ascp
updated by GenoMax GenoMax • written by wzzzling • wzzzling
0 votes
1 reply
971 views
Run TSS predator without TEX wig libraries
rna-seq sequencing next-gen software error
updated by mwittep • mwittep • written by qstefano • qstefano
0 votes
1 reply
683 views
Anyone have knowledge of TSS Predator ??
usage predator prediction plants tss
updated by mwittep • mwittep • written by nikhil • nikhil
0 votes
2 replies
219 views
How to get mouse genomes to test CNV tools with?
cnv grcm39 genome mouse cnvtools
written by Pipschroma • Pipschroma
0 votes
1 reply
218 views
Issues with the new PHASTEST web tool
phages draft-genomes
updated by Roshan • Roshan • written by anna.licitra • anna.licitra
0 votes
0 replies
79 views
GSEA for metagenomic data
ora metagenome deseq2 gsea fgsea
written by young_bioinformatician young_bioinformatician
0 votes
2 replies
348 views
MEGAHIT assembly k-mer exceeds read length – is the result still reliable?
megahit assembly
written by vibryschaan • vibryschaan
0 votes
4 replies
887 views
News: FINAL CALL - 10th Berlin Summer School in NGS Data Analysis (June 2026, in-person, Berlin)
fastq variantcalling differentialexpression bam
written by ecSeq Bioinformatics • ecSeq Bioinformatics
0 votes
7 replies
672 views
Aligning short reads using STAR
rna-seq alignment splice star deseq2
updated by LauferVA LauferVA • written by bm.nina • bm.nina
0 votes
0 replies
57 views
Missing ML/PL FORMAT fields in GVCFtyper joint calling output (Ultima Genomics + DNAscope)
jointcalling ultimawgs
updated by GenoMax GenoMax • written by SeoG • SeoG
2 votes
15 replies
5.1K views
fast way to get last position in a large indexed VCF?
bcftools
updated by bgulko2 • bgulko2 • written by curious curious
0 votes
3 replies
294 views
Formatting annotated genomes for submission to NCBI
ontology genome sequin protein submission hypothetical
written by jaredbernard • jaredbernard
0 votes
0 replies
60 views
Help with find_circ troubles
circrna find_circ
written by Eduarda • Eduarda
0 votes
1 reply
127 views
Tool: Stargazer - open-source, agentic workflow orchestration for computational biologists
orchestration
updated by ATpoint ATpoint • written by pryce.turner • pryce.turner
0 votes
1 reply
240 views
News: Courses on Spatial Omics in 2026
singlecell spatialomics computationalbiology
written by Physalia-courses Physalia-courses
0 votes
1 reply
144 views
DNASeq pipeline analysis
rna dneseq
updated by ATpoint ATpoint • written by SHN • SHN
1 vote
18 replies
17K views
Hifiasm is getting killed while trying to assemble a genome
assembly genome hifiasm
updated by Bharat K. C. Patel • Bharat K. C. Patel • written by pranavdatar01 • pranavdatar01
0 votes
2 replies
249 views
Tutorial: Stop writing ggplot2 code. Make publication figures directly in Excel
ggplot excel statistic visualization r
written by Aki • Aki
0 votes
3 replies
336 views
VG Crash with HPRC V2.0 Graph and Indexes
vg
updated by Jouni Sirén Jouni Sirén • written by Alexandria A. • Alexandria A.
1 vote
2 replies
201 views
News: Recurring amino acid clustering pattern in >160,000 protein structures: looking for independent visual confirmation
bioinformatics amino-acids citizen-science protein-structure structural-biology
written by FranciscoJLoboCab • FranciscoJLoboCab
0 votes
3 replies
382 views
GATK SNP calling from BAM
vg
updated by dario.galanti92 • dario.galanti92 • written by zhengluo • zhengluo
0 votes
0 replies
45 views
Ligand breaking after docking
error docking
written by avnim • avnim
0 votes
4 replies
268 views
Kallisto low alignment rate
rna rnaseq kallisto
updated by dsull dsull • written by Gerard • Gerard
0 votes
5 replies
275 views
Does increased heterozygosity from contaminating DNA lead to over-estimated KING relatedness?
king heterozygosity kinship relatedness contamination
written by Joel Wallenius Joel Wallenius
0 votes
4 replies
271 views
how to convert whole genome sequencing datasets to use for GWAS
gwas gapit r
written by ngseq • ngseq
0 votes
0 replies
116 views
News: Causal AI Methods for Computational Biology
casualinference computationalbiology ai
written by Physalia-courses Physalia-courses
0 votes
3 replies
172 views
Impact of HPO term completeness on Exomiser ranking
genomics sequencing analysis ngs
written by sameer • sameer
0 votes
2 replies
152 views
DP distribution plotting
filtering dp distribution vcf
written by Floky • Floky
0 votes
1 reply
114 views
Query on graph analysis and understanding
graph-analysis
updated by Ram Ram • written by Ekta • Ekta
1 vote
8 replies
364 views
An exon frameshift that doesn't effect the gene?
exon frameshift
written by Jaden • Jaden
0 votes
8 replies
445 views
How dispersion is used in EdgeR
edger regression binomial negative dispersion
updated by Gordon Smyth Gordon Smyth • written by joelking • joelking
0 votes
2 replies
491 views
Best way to extract SNPs and INDEL from multiple samples
gwas wgs ngs
written by ngseq • ngseq
0 votes
2 replies
277 views
Practice for combining multiple host genomes for BWA host removal
bwa removal host
updated by GenoMax GenoMax • written by jay • jay
6 votes
22 replies
1.4K views
Forum: What is your best "If only I'd known about this feature sooner" moment?
software igv
updated by Stefanie • Stefanie • written by crisime crisime
0 votes
19 replies
4.4K views
MacOS Quicklook plugin for gtf and gff3 files?
gtf gff3 macos
written by kalavattam • kalavattam
0 votes
3 replies
219 views
BWA MEM output has read1 sequence written into read2 record — input FASTQs are correctly paired
bwa
written by vibryschaan • vibryschaan
0 votes
0 replies
49 views
Should depot (tissue type) be included as a covariate in batch effect correction for bulk RNA-seq data?
batcheffect rnasequencing transcriptomics
written by Dimitris • Dimitris
0 votes
0 replies
70 views
questions about loeuf plugin setup for VEP tool
vep_tool vep loeuf ensembl
written by evbat • evbat
0 votes
1 reply
142 views
Filtering KofamScan output for KEGGDecoder usage
shotgun data mags keggdecoder kofamscan
updated by andres.firrincieli andres.firrincieli • written by sveta5678 • sveta5678
0 votes
1 reply
99 views
How to amplify prey cDNA library for Yeast two Hybrid (y2h)?
y2h
updated by GenoMax GenoMax • written by Usama • Usama
1 vote
3 replies
231 views
Does TCGA actually have germline vcfs?
mutations germline tcga
updated by LauferVA LauferVA • written by mrk • mrk
0 votes
1 reply
97 views
rnaseq trimming
trimming rnaseq
updated by GenoMax GenoMax • written by murheisa • murheisa
0 votes
1 reply
82 views
merging chromosome zarr stores - will this work?
zarr python scikit-allel
updated by GenoMax GenoMax • written by mcrepeau • mcrepeau
0 votes
0 replies
36 views
Mapping taxa with moderate to sparse loci coverage to reference backbone tree
downstream analysis
written by katstancity • katstancity
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