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HIC-pro with Forward and reverse reads not paired even when I use their test data.
HIC-pro
1 hour ago by Aki ▴ 20
0
votes
1
reply
199
views
Using DEXseq on kallisto tsv outputs ?
alignement DEXseq kallisto
updated 3 hours ago by ★ 7.9k • written 5 days ago by ▴ 10
0
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0
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43
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Job: 2025 Arrowhead AI/LLM for Computational Biology and Data Science Internship
intern
updated 6 hours ago by 150k • written 6 hours ago by ★ 9.6k
1
vote
2
replies
418
views
ChIP-seq gene blacklist for Rattus norvegicus
rat blacklist ChIP-seq
updated 6 hours ago by 150k • written 12 months ago by • 0
4
votes
10
replies
731
views
6 follow
Extract length of sample sequence from vcf
microsatellites bcftools vcf indels variants
updated 8 hours ago by ★ 4.2k • written 10 days ago by • 0
836
votes
167
replies
173k
views
111 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 1 day ago by 3.4k • written 8.4 years ago by 102k
0
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0
replies
60
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Tutorial: Fast SCENIC GRN Analysis with RegDiffusion
GRN network scRNA-seq wgcna
10 hours ago by Hao ▴ 10
2
votes
3
replies
475
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Is it reasonable to do "Gene Regulatory Network Inference" for each cell type and do differential GRN
GRN scRNA-seq
updated 9 hours ago by ▴ 10 • written 2.6 years ago by ▴ 30
1
vote
2
replies
251
views
Blastx issue
Long coding non blastx RNA
updated 10 hours ago by 7.4k • written 3 days ago by • 0
0
votes
5
replies
332
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TPM vs FPKM divergence at high values
tpm fpkm normalisation
updated 11 hours ago by 102k • written 2 days ago by • 0
2
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0
replies
67
views
Herald: The Biostar Herald for Monday, April 14, 2025
herald
11 hours ago by Biostar 3.4k
0
votes
1
reply
195
views
What is the best way to know if a pair of genes is random?
terms genes go
updated 12 hours ago by ★ 1.5k • written 3 days ago by • 0
0
votes
1
reply
172
views
How to save the AlphaFold PAE plot as an image in ChimeraX using command line ?
PAE ChimeraX AlphaFold
updated 12 hours ago by 4.7k • written 2 days ago by ▴ 680
1
vote
0
replies
60
views
News: Building an mmCIF parser for enzyme structure analysis — feedback & ideas welcome!
mmcif
updated 13 hours ago by 150k • written 16 hours ago by • 0
1
vote
0
replies
68
views
News: LAST CALL - Bioinformatics Pipeline Development with Nextflow - May 19-21, 2025 (online) - Apply Now
nextflow rnaseq workshop
16 hours ago by ecSeq Bioinformatics ▴ 20
1
vote
2
replies
177
views
RNA-seq, three comparisons - stick to one linear model, or use separate models?
statistics mixed_effect_model linear_model stats RNAseq
8 hours ago by noodlejackson ▴ 40
0
votes
1
reply
104
views
Using Principal Components may muddle the detecting power of a GWAS?
q-value covariates genomic-inflation pca gwas
updated 17 hours ago by ▴ 470 • written 19 hours ago by • 0
0
votes
0
replies
79
views
Use Seed or Full Alignments from Pfam HMM as a filter step
hmm sequences metagenomic
19 hours ago by Janelyn123 • 0
1
vote
4
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224
views
Helicobacter pylori low-rate alignment
bioinformatics transcriptomics RNA-seq
updated 10 hours ago by 150k • written 1 day ago by ▴ 20
14
votes
3
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11k
views
Can The Wget Command Be Used To Download Pdbs
pdb
updated 20 hours ago by • 0 • written 13.5 years ago by ▴ 310
0
votes
3
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259
views
Is a log2 transformation an essential step in preparing expression data for machine learning?
Machinelearning microarray preproccessing
updated 1 day ago by ★ 29k • written 1 day ago by ▴ 60
0
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2
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852
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How to re-annotate the structure of gene against a known genomic file
RNA-Seq
updated 1 day ago by ★ 29k • written 5.9 years ago by • 0
0
votes
1
reply
184
views
ONT Live-Basecalling Issue?
ONT minKNOW live-basecalling
updated 1 day ago by 150k • written 2 days ago by • 0
3
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4
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262
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Identify gene from sequence at scale in non-model organisms
name sequence gene
updated 1 day ago by ★ 1.5k • written 2 days ago by • 0
0
votes
0
replies
128
views
News: Cellosaurus release 52 is available
database line cell knowledgebase biocuration
2 days ago by Amos Bairoch ▴ 130
0
votes
2
replies
251
views
WGCNA
problem
updated 2 days ago by 150k • written 3 days ago by • 0
0
votes
0
replies
239
views
Seeking Advice on Causal Inference for Treatment Effect Prediction (Small Sample, Genomic Covariates)
inference causal
2 days ago by oghzzang ▴ 50
5
votes
5
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429
views
Batch effect
RNAseq Batch-Effect
1 day ago by Fatemeh ▴ 40
0
votes
4
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366
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convert Gene ID to Gene Symbol
gene-id
updated 2 days ago by ▴ 110 • written 5 days ago by • 0
0
votes
1
reply
193
views
News: Structural bioinformatics workshop
Structural bioinformatics
updated 3 days ago by 150k • written 3 days ago by • 0
1
vote
10
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545
views
How to test the similarity of two gene expression profiles
test gene sets
updated 2 days ago by ▴ 130 • written 4 days ago by • 0
3
votes
3
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229
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Which are the different kinds of GeneID that exist?
R RNA-Seq
3 days ago by pinheirofabiano ▴ 110
0
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0
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143
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Error using DWLS
deconvolution DWLS RNAseq
3 days ago by Ana • 0
0
votes
5
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1.7k
views
How to remove this module selection error?
WGCNA
updated 3 days ago by • 0 • written 2.3 years ago by • 0
0
votes
1
reply
865
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 3 days ago by 150k • written 3 days ago by ▴ 590
1
vote
2
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216
views
Limma for DEG aalysis
R DEG limma ANALYSIS
3 days ago by rahma.khoualdia • 0
0
votes
0
replies
180
views
deletion impact
vcf
updated 3 days ago by 150k • written 3 days ago by • 0
0
votes
2
replies
235
views
Help finding GTEx v8 file
GTEx SHAPEIT2
2 days ago by 蒲蒲 • 0
2
votes
5
replies
285
views
Idat file processing issue with command line cli
CanineHTS IDAT
3 days ago by 1769mkc ★ 1.2k
0
votes
0
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150
views
is there a way to get --ref paths to prioritize my order with vg call?
call vg vgcall
1 hour ago by PolenP • 0
0
votes
1
reply
209
views
Has anyone tried used simple ML models to identify virulence genes?
genetics R classifier genomics machinelearning
updated 3 days ago by ★ 29k • written 4 days ago by • 0
0
votes
4
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325
views
What does vg autoindex mpmap do?
vg mpmap autoindex
12 hours ago by Ziyue • 0
5
votes
4
replies
369
views
How to keep the same view for different AlphaFold 3 simulations in ChimeraX?
chimerax alphafold 3
updated 3 days ago by 4.7k • written 4 days ago by ▴ 680
0
votes
0
replies
170
views
filtering genes before or after the correlation?
co-expression feature selection correlation
4 days ago by tyasird ▴ 10
0
votes
16
replies
733
views
Which tools use or rely on the XA tag in SAM/BAM/CRAM files?
cram XA compress
updated 3 days ago by ▴ 130 • written 5 days ago by • 0
2
votes
4
replies
290
views
Which additional files are needed for the -taxids option in blast?
decontamination taxids blastn
updated 4 days ago by 150k • written 4 days ago by • 0
0
votes
0
replies
186
views
Job: Assistant, Associate, or Full Project Scientist in Neurobiology
Biology Neuroscience Neurobiology
4 days ago by UCSDBioSci ▴ 30
1
vote
3
replies
301
views
Is Centering and Scaling Essential for Expression Data as Input for Machine Learning Algorithms?
featureselection microarray preprocessing
1 day ago by Sib ▴ 60
0
votes
0
replies
194
views
News: Online Course: Machine learning for multi-omics integration (9–11 June)
Machine-Learning Mult-Omics
4 days ago by Physalia-courses ★ 2.6k
0
votes
2
replies
273
views
Single Nuclei RNA-Sequencing Analysis Without CellRanger
CellRanger single-cell snRNA-seq
3 days ago by 16_masques.vole • 0
120,980 results • Page 1 of 2420
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How to keep the same view for different AlphaFold 3 simulations in ChimeraX?
Answer: How to keep the same view for different AlphaFold 3 simulations in ChimeraX?
Answer: Chip-seq Analysis
Comment: ChIP-seq gene blacklist for Rattus norvegicus
C: Filtering a multi-person structural variant VCF file by type of SV
Comment: Helicobacter pylori low-rate alignment
STAR aligner - Is this still maintained?
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Recent Replies
Answer: Using DEXseq on kallisto tsv outputs ? by Gordon Smyth ★ 7.9k
Inputting transcript (RNA isoform) quantifications from kallisto into tools like DEXSeq that are designed for exons is not ideal because th…
Comment: ChIP-seq gene blacklist for Rattus norvegicus by GenoMax 150k
https://kilthub.cmu.edu/articles/dataset/Alternate_gene_annotations_for_rat_macaque_and_marmoset_for_single_cell_RNA_and_ATAC_analyses/2117…
Comment: ChIP-seq gene blacklist for Rattus norvegicus by RD ▴ 20
Were you able to find the list of regions? Thank you!
Comment: Extracting Variant Sequences from 1000 Genomes VCF File and Mapping to Canonical by cmdcolin ★ 4.2k
doesn't solve your problem exactly but I stumbled on this blog post awhile back https://kalis.louisaslett.com/articles/lct_example.html#re…
Answer: Extract length of sample sequence from vcf by cmdcolin ★ 4.2k
Not sure if it helps but I saw this impressive one-liner in a blog post that 'reconstructs the sequence for the 1000 genomes samples' http…
Comment: RNA-seq, three comparisons - stick to one linear model, or use separate models? by noodlejackson ▴ 40
Thank you @ATpoint
Comment: Is it reasonable to do "Gene Regulatory Network Inference" for each cell type an by Hao ▴ 10
it's a bioarxiv so I didn't provide the link. Anyway, link added and I changed the language.
Comment: Is it reasonable to do "Gene Regulatory Network Inference" for each cell type an by GenoMax 150k
Please edit the answer above and provide a link (either PubMed or direct journal) for the paper. Just saying you did "X" is not providing a…
Comment: Helicobacter pylori low-rate alignment by GenoMax 150k
> What is the best trade off in this scenario? As noted earlier, this data is ~ 15 yr old at this point i.e. from the dawn of NGS tech. It…
Answer: Is it reasonable to do "Gene Regulatory Network Inference" for each cell type an by Hao ▴ 10
Sure. In [one of our preprints][1], we did sort of a similar thing on cells from different time points. [1]: https://www.biorxiv.org/c…
Answer: Blastx issue by colindaven 7.4k
You could also use an ORF finder like transdecoder or prodigal as an additional check. Many lncRNAs might have very short ORFs, but are unl…
Answer: TPM vs FPKM divergence at high values by Istvan Albert 102k
Both TPM and FPKM will normalize to the so-called "library size", which is how many mapped reads are in each sample. So, that is not what c…
Comment: Extract length of sample sequence from vcf by Istvan Albert 102k
make sure the variants are normalized and properly decomposed, also maybe show that VCF row as well, This example you gave seems to show…
Comment: Helicobacter pylori low-rate alignment by GenoMax 150k
> using bowtie 2 and the genomic annotation taken from https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000008525.1/ Did you see folowing …
Answer: What is the best way to know if a pair of genes is random? by shelkmike ★ 1.5k
I don't know about the best way, but one method to do this, I think, could look as follows:<br> 1) Take all possible pairs of genes and fo…
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