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1 vote
5 replies
2.0K views
Why don't I see people calculating FPKM from normalized read counts?
normalization rna-seq
updated by kalavattam • kalavattam • written by shelkmike shelkmike
0 votes
9 replies
2.7K views
Error during running wf-bacterial-genome (nextflow run epi2me-labs/wf-bacterial-genomes).
epi2me medaka
updated by GenoMax GenoMax • written by Anurag • Anurag
0 votes
0 replies
777 views
freebayes with pools of different number of individuals
freebayes poolseq
written by Jeanlain • Jeanlain
0 votes
3 replies
1.3K views
Insight into Trimmomatic
trimmomatic trimming reads
updated by GenoMax GenoMax • written by jh5ym • jh5ym
0 votes
3 replies
2.0K views
Trouble when uploading FASTQ files on NCBI
rnaseq ncbi
written by Gerard • Gerard
0 votes
4 replies
2.0K views
SyntaxError in file /snakefile, line 22: invalid decimal literal: None
python snakemake
updated by Jesse • Jesse • written by Ana • Ana
1 vote
2 replies
1.5K views
News: Building an mmCIF parser for enzyme structure analysis — feedback & ideas welcome!
mmcif
written by Shravya • Shravya
0 votes
0 replies
1.0K views
News: Course: Introduction to Genome Annotation (Online, 19–22 May) - last call
gene-prediction genome-annotation gene-models
written by Physalia-courses Physalia-courses
0 votes
1 reply
1.2K views
Error with running cellranger-atac count
cellranger atac single-cell
updated by Ram Ram • written by Khôi • Khôi
0 votes
2 replies
1.5K views
HIC-pro with Forward and reverse reads not paired even when I use their test data.
hic-pro
written by Aki • Aki
0 votes
1 reply
1.1K views
Using DEXseq on kallisto tsv outputs ?
alignement dexseq kallisto
updated by Gordon Smyth Gordon Smyth • written by Gerard • Gerard
0 votes
1 reply
1.9K views
Job: 2025 Arrowhead AI/LLM for Computational Biology and Data Science Internship
intern
updated by Simon • Simon • written by Shicheng Guo Shicheng Guo
0 votes
2 replies
1.5K views
ChIP-seq gene blacklist for Rattus norvegicus
rat blacklist chip-seq
updated by GenoMax GenoMax • written by Thomas • Thomas
0 votes
10 replies
3.4K views
Extract length of sample sequence from vcf
microsatellites bcftools vcf indels variants
updated by cmdcolin cmdcolin • written by jahnreinhard.ringger • jahnreinhard.ringger
0 votes
3 replies
1.6K views
Is it reasonable to do "Gene Regulatory Network Inference" for each cell type and do differential GRN
grn scrna-seq
updated by Hao • Hao • written by shangguandong1996 • shangguandong1996
0 votes
2 replies
1.2K views
Blastx issue
blastx lncrna
updated by Ram Ram • written by Avik • Avik
0 votes
9 replies
3.0K views
TPM vs FPKM divergence at high values
tpm fpkm normalisation
updated by Istvan Albert Istvan Albert • written by megancgrdnr • megancgrdnr
3 votes
0 replies
26K views
Herald: The Biostar Herald for Monday, April 14, 2025
herald
written by Biostar Biostar
1 vote
5 replies
1.5K views
What is the best way to know if a pair of genes is random?
go-terms genes
written by Ana • Ana
0 votes
1 reply
1.6K views
How to save the AlphaFold PAE plot as an image in ChimeraX using command line ?
pae chimerax alphafold
updated by LauferVA LauferVA • written by Picasa Picasa
1 vote
0 replies
838 views
News: LAST CALL - Bioinformatics Pipeline Development with Nextflow - May 19-21, 2025 (online) - Apply Now
nextflow rnaseq workshop
written by ecSeq Bioinformatics • ecSeq Bioinformatics
0 votes
2 replies
1.0K views
RNA-seq, three comparisons - stick to one linear model, or use separate models?
statistics mixed-effect-model stats rnaseq linear-model
updated by Ram Ram • written by noodlejackson • noodlejackson
0 votes
1 reply
1.1K views
Using Principal Components may muddle the detecting power of a GWAS?
q-value covariates genomic-inflation pca gwas
updated by DBScan • DBScan • written by Noctiluca • Noctiluca
0 votes
0 replies
645 views
Use Seed or Full Alignments from Pfam HMM as a filter step
hmm sequences metagenomic
written by Jane123 • Jane123
0 votes
4 replies
1.2K views
Helicobacter pylori low-rate alignment
rna-seq transcriptomics
updated by Ram Ram • written by Ariadna • Ariadna
2 votes
3 replies
12K views
Can The Wget Command Be Used To Download Pdbs
pdb
updated by Calvin • Calvin • written by Harpalss Harpalss
0 votes
3 replies
1.4K views
Is a log2 transformation an essential step in preparing expression data for machine learning?
machine-learning preproccessing microarray
updated by Ram Ram • written by Sib • Sib
0 votes
2 replies
1.4K views
How to re-annotate the structure of gene against a known genomic file
rna-seq
updated by Mensur Dlakic Mensur Dlakic • written by Kanoo • Kanoo
0 votes
2 replies
1.2K views
ONT Live-Basecalling Issue?
ont minknow live-basecalling
updated by LauferVA LauferVA • written by Akshay • Akshay
0 votes
4 replies
1.2K views
Identify gene from sequence at scale in non-model organisms
sequence gene
updated by Ram Ram • written by matthewmerkin32 • matthewmerkin32
0 votes
0 replies
704 views
News: Cellosaurus release 52 is available
biocuration database knowledgebase cell-line
updated by Ram Ram • written by Amos Bairoch • Amos Bairoch
0 votes
2 replies
1.3K views
WGCNA
wgcna
updated by Ram Ram • written by 香 • 香
0 votes
0 replies
878 views
Seeking Advice on Causal Inference for Treatment Effect Prediction (Small Sample, Genomic Covariates)
causal-inference
updated by Ram Ram • written by oghzzang • oghzzang
1 vote
5 replies
1.4K views
Batch effect
rnaseq batch-effect
written by Fatemeh • Fatemeh
0 votes
4 replies
1.3K views
convert Gene ID to Gene Symbol
gene-id
updated by pinheirofabiano • pinheirofabiano • written by majorprogeria • majorprogeria
0 votes
1 reply
721 views
News: Structural bioinformatics workshop
structural-bioinformatics
updated by Ram Ram • written by reetesh • reetesh
0 votes
10 replies
1.8K views
How to test the similarity of two gene expression profiles
gene-sets
updated by Ram Ram • written by htchd • htchd
0 votes
3 replies
1.1K views
Which are the different kinds of GeneID that exist?
r rna-seq
written by pinheirofabiano • pinheirofabiano
0 votes
0 replies
590 views
Error using DWLS
deconvolution dwls rnaseq
written by Ana • Ana
0 votes
5 replies
2.5K views
How to remove this module selection error?
wgcna
updated by 香 • 香 • written by gupta00aritra • gupta00aritra
0 votes
2 replies
2.3K views
bbsplit : How to configure ambiguous/ambiguous2 parameters in order to consider as unmapped reads, reads mapped on both human/mouse references.
bbsplit nextflow
updated by GenoMax GenoMax • written by ZheFrench ZheFrench
0 votes
2 replies
1.2K views
Limma for DEG analysis
r deg limma
updated by Ram Ram • written by rahma.khoualdia • rahma.khoualdia
0 votes
0 replies
626 views
deletion impact
vcf
updated by GenoMax GenoMax • written by HarperReed • HarperReed
0 votes
2 replies
1.0K views
Help finding GTEx v8 file
gtex shapeit2
written by 蒲蒲 • 蒲蒲
0 votes
5 replies
1.4K views
Idat file processing issue with command line cli
caninehts idat
written by 1769mkc 1769mkc
0 votes
0 replies
708 views
is there a way to get --ref paths to prioritize my order with vg call?
call vg vgcall
written by PolenP • PolenP
0 votes
1 reply
881 views
Has anyone tried used simple ML models to identify virulence genes?
genetics r classifier genomics machinelearning
updated by Mensur Dlakic Mensur Dlakic • written by Jack • Jack
0 votes
4 replies
1.7K views
What does vg autoindex mpmap do?
vg mpmap autoindex
written by Ziyue • Ziyue
1 vote
4 replies
2.4K views
How to keep the same view for different AlphaFold 3 simulations in ChimeraX?
chimerax alphafold 3
updated by LauferVA LauferVA • written by Picasa Picasa
0 votes
0 replies
595 views
filtering genes before or after the correlation?
co-expression feature selection correlation
written by tyasird • tyasird
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