This is a test version of Biostars. For the public version, visit https://www.biostars.org.
0 votes
1 reply
85 views
GenomicsDBImport completes successfully, but SelectVariants/GenotypeGVCFs hangs at “Starting traversal” when reading gendb:// workspace
gatk
updated by fernando • fernando • written by chiyong4783 • chiyong4783
0 votes
4 replies
272 views
Error while doing joint genotype calling using GATK
snps gatk gwas wgs
written by ngseq • ngseq
0 votes
0 replies
53 views
News: Cancer Genomics workshop - online, 27–29 April
precisiononcology cancergenomics
written by Physalia-courses Physalia-courses
0 votes
8 replies
608 views
Liftover failure with UCSC from hg38 to hg19
ucsc hg19 hg38 liftover
updated by Maximilian Haeussler Maximilian Haeussler • written by _quantum_girl_ • _quantum_girl_
0 votes
0 replies
124 views
Job: Assistant, Associate, or Full Project Scientist in Molecular Biology
ucsd biology
written by UCSDBioSci • UCSDBioSci
2 votes
0 replies
118 views
Tool: vcfkit — open-source Rust CLI for VCF normalize, liftover, and filter (4× faster than bcftools on filter)
rust vcf normalize filter liftover
written by Prasad • Prasad
0 votes
4 replies
454 views
differential gene expression analysis (samples number)
expression differential analysis gene
updated by swbarnes2 swbarnes2 • written by Hossam • Hossam
0 votes
9 replies
2.7K views
Tool: A python library for reading and writing sequences in fasta and fastq format.
seqio
updated by Istvan Albert Istvan Albert • written by dwpeng • dwpeng
1 vote
5 replies
625 views
Forum: Advice for transitioning from a Life Sciences Education degree to Bioinformatics
life bioinformatics sciences masters education
updated by Bharat K. C. Patel • Bharat K. C. Patel • written by mireader11 • mireader11
0 votes
1 reply
979 views
fgbio read structure
fgbio umi extractumisfrombam
updated by farha • farha • written by MH85 • MH85
0 votes
2 replies
254 views
Extracting individual chromosomes from a .gfa graph
xg vg gfa chunk
written by samuel.michel • samuel.michel
2 votes
1 reply
173 views
Tool: 17 pre-configured pixi environments for microbial genomics — built by a biologist, not a developer
installation reproducibility pixi genomics snakemake
written by Bharat K. C. Patel • Bharat K. C. Patel
1 vote
1 reply
375 views
Job: Bioinformatics Programmer I ( Genomic Medicine) Houston, TX, United States
bioinformatics python medicine pipelines ngs
updated by Ram Ram • written by bioinformatics • bioinformatics
1 vote
0 replies
149 views
Tutorial: Running spaceranger segment for Visium HD QC on Windows (WSL2) — workflow + QuPath script
wsl2 qupath spaceranger 10x-genmoics windows
updated by lauraashaley • lauraashaley • written by Jing-Yuan • Jing-Yuan
2 votes
1 reply
98 views
Global changes in TE expression, how to normalize?
deseq2
updated by lauraashaley • lauraashaley • written by Michael Love Michael Love
0 votes
1 reply
138 views
Test data for benchmarking a pipeline
nextflow isolate pipeline metagenomics wgs
updated by GenoMax GenoMax • written by zizigolu zizigolu
2 votes
1 reply
79 views
News: Boost your data analysis skills – Discover the Physalia May courses
bioinformatics rnaseq gwas genomics statistics
updated by lauraashaley • lauraashaley • written by Physalia-courses Physalia-courses
1 vote
3 replies
347 views
Liftoff feature mapping
annotation liftoff
updated by lauraashaley • lauraashaley • written by Christopher • Christopher
1 vote
2 replies
1.6K views
Demultiplex PacBio CCS reads on Mac
pacbio demultiplex next-gen sequencing
updated by lauraashaley • lauraashaley • written by manthony5955 • manthony5955
1 vote
5 replies
381 views
How should I define output for a Nextflow demultiplexing rule?
hifi lima demultiplexing nextflow
written by sholt6 • sholt6
1 vote
9 replies
624 views
How to interpret segmental duplications in UCSC browser?
duplications browser ucsc
updated by lauraashaley • lauraashaley • written by _quantum_girl_ • _quantum_girl_
5 votes
5 replies
418 views
Forum: AI era of the forum
ia
updated by lauraashaley • lauraashaley • written by Juke34 Juke34
4 votes
1 reply
134 views
Tool: vareffect — a Rust-based variant effect predictor that replaces VEP
rust vcf hgvs variant-annotation vep
updated by lauraashaley • lauraashaley • written by LIA Genomics • LIA Genomics
1 vote
2 replies
215 views
gene-expression data from RNA-seq
gene-expression rna-seq
updated by i.sudbery i.sudbery • written by yana • yana
1 vote
3 replies
2.0K views
Nextflow crash on AWS Batch with transition error
bwa nextflow aws
updated by lauraashaley • lauraashaley • written by hkarakurt hkarakurt
1 vote
16 replies
3.8K views
The Best Cloud Solution For Genomics
workflow data-sharing paas genomics cloud
updated by lauraashaley • lauraashaley • written by davidmaimoun • davidmaimoun
3 votes
1 reply
136 views
Tool: PERREO: An integrated pipeline for repetitive elements analysis enables the repeatome expression profiling in cancer
repeatome bioinformatics rna-seq
updated by lauraashaley • lauraashaley • written by frarodmar17 • frarodmar17
1 vote
1 reply
134 views
News: (Online course) Agentic AI for Life Sciences
genomics ai agenticai
updated by lauraashaley • lauraashaley • written by Physalia-courses Physalia-courses
1 vote
3 replies
663 views
CIBERSORTx analysis
seq cibersortx scrna
updated by HEMANT • HEMANT • written by yadavsoumya647 • yadavsoumya647
13 votes
28 replies
14K views
How Much Does It Cost To Align A Flowcell In The Cloud?
cloud
updated by Antonio R. Franco Antonio R. Franco • written by Jeremy Leipzig Jeremy Leipzig
0 votes
1 reply
1.1K views
Azure vs AWS for cloud computing with Kraken2?
aws azure metagenomics kraken2
updated by Nishika • Nishika • written by Natalia • Natalia
0 votes
18 replies
2.1K views
NCBI Genomes submission - what to do if FCS report is incorrect? Stuck with nowhere to go!! No communication!
ncbi submissions genomes
updated by MirianT_NCBI • MirianT_NCBI • written by susan.klein • susan.klein
0 votes
0 replies
76 views
Tool: FAIRMD Lipids Databank web-portal, seeking feedback
data molecular-dynamics membranes lipids bilayer
written by Michael Dondrup Michael Dondrup
7 votes
17 replies
9.5K views
Do I Have A Chance To Hire A Bioinformatics Freelancer?
freelance
updated by Michael Dondrup Michael Dondrup • written by Pawel Szczesny Pawel Szczesny
0 votes
1 reply
226 views
Can PC1 (eigengenes) from different gene sets be compared in WGCNA/hdWGCNA?
hdwgcna eigengene module wgcna
updated by andres.firrincieli andres.firrincieli • written by Shriyansh • Shriyansh
1 vote
4 replies
3.4K views
Tool for extracting part of aligned sequence by CIGAR string
cigar sam bam extract alignment
updated by Marek • Marek • written by Charles-Alexandre Roy • Charles-Alexandre Roy
5 votes
14 replies
1.4K views
Tool: RustQC: 60x speedup in RNA-seq quality control steps
rustqc nf-core
updated by jared.andrews07 jared.andrews07 • written by Phil Ewels Phil Ewels
0 votes
0 replies
73 views
Peptidomics Quality Control
peptidomics control quality proteomics ms
written by fnepo • fnepo
0 votes
0 replies
72 views
Merging Serial Matrix file with 1240k AADR data set.
aadr
updated by GenoMax GenoMax • written by avirmed006 • avirmed006
0 votes
0 replies
65 views
WOMBAT for multitrait GWAS analysis
gwas multitrait wombat
written by Bushra Bibi Bushra Bibi
1 vote
15 replies
7.6K views
Forum: How to decide when to have local hardware vs cloud computing?
hardware computational-resources cloud
updated by i.sudbery i.sudbery • written by Lluís R. Lluís R.
0 votes
10 replies
8.8K views
Using AWS for Bioinformatics
unix cluster
updated by Nishika • Nishika • written by dk0319 • dk0319
0 votes
4 replies
396 views
Problem trimming SAM file to use with assembler
fastq sam assembly
updated by GenoMax GenoMax • written by Emilio • Emilio
0 votes
2 replies
272 views
Issue when using design matrix taking batch effect into account - EdgeR RNA-seq
rna-seq edger design-matrix
updated by Ram Ram • written by maxime • maxime
0 votes
5 replies
440 views
Liftover from one yeast species into another one fails
vcf chain chainfile liftover gatk
updated by GenoMax GenoMax • written by Iseez • Iseez
0 votes
0 replies
88 views
News: Workshop: Virtual Genome Annotation, May 19-21, 2026
genomeannotation workshop uconn
written by zsc25001 • zsc25001
0 votes
0 replies
276 views
Job: Founding Computational Biologist, AI Agents for Pharma
bioinformatics discovery llm drug pharma
updated by colindaven colindaven • written by iollo Hiring Team • iollo Hiring Team
0 votes
7 replies
568 views
How to merge SNP datasets aligned to different reference genome versions without re-calling variants?
genome-assembly vcf snp variant-calling liftover
written by jhonatan.henrique • jhonatan.henrique
0 votes
0 replies
90 views
Tool: Advit: An automated, cross-platform pipeline for Kraken2/Bracken classification and Krona visualization
kraken metagenomics
written by Rounak • Rounak
0 votes
0 replies
55 views
News: Workshop:Virtual Genome Assembly, April 21-23, 2026
virtual genomeassembly workshop uconn
written by zsc25001 • zsc25001
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