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Identifying gene outliers in a genome using composition analysis.
RSCU composition GC outliers
1 hour ago by Shakunthala Natarajan • 0
0
votes
0
replies
18
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Mapping to a template sequece
sequencing
1 hour ago by QX ▴ 70
0
votes
1
reply
131
views
quality control for 16s metagenome reads
quality metagneome control 16s fastp
updated 2 hours ago by 10k • written 2 days ago by ▴ 30
0
votes
2
replies
141
views
Loss of strandedness in the Illumina Strandedness Total RNA protocol
Illumina RNA-seq reads stranded
updated 3 hours ago by 88k • written 9 hours ago by ▴ 840
1
vote
2
replies
839
views
Problem with Mirdeep2 and Randfold output
mirdeep2 Randfold
updated 14 hours ago by • 0 • written 14 months ago by ▴ 40
0
votes
0
replies
106
views
Help using ShinyCell2 and Seurat v5 object.
shinycell seurat shiny shinycell2 scRNA
19 hours ago by Jamie • 0
0
votes
0
replies
72
views
News: Machine Learning for Multi-Omics Integration at the University of Barcelona– Dec 2025
Machine-Learning Sulti-Omics Depp-Learning Data-Integration BigData
20 hours ago by Physalia-courses ★ 2.6k
843
votes
170
replies
182k
views
112 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 10 weeks ago by 3.6k • written 8.6 years ago by 102k
0
votes
0
replies
103
views
Compare alternative splicing patterns between human and mouse?
orthologs rna-seq splicing alternative
20 hours ago by aeb ▴ 20
2
votes
3
replies
175
views
Trouble getting representatives from clustered_nr database
database blast
updated 15 hours ago by 152k • written 21 hours ago by • 0
0
votes
0
replies
86
views
FindTransferAnchors (reference prediction) vs Manual Annotations
Seurat
21 hours ago by reddyornah • 0
0
votes
6
replies
297
views
Which Reference Hg38 or T2T?? Both??
Host Removal
8 hours ago by Jon • 0
3
votes
4
replies
229
views
NCBI Datasets CLI Question
ncbi-datasets
1 day ago by Bjorn • 0
0
votes
0
replies
107
views
Incomplete assembly in HPRC dataset
pangenome HPRC reference
1 day ago by ohell • 0
3
votes
3
replies
231
views
Joint Calling for Large Germline WGS Cohort
NGS RAM cohort Genomics WGS
updated 1 day ago by 23k • written 2 days ago by ▴ 20
0
votes
4
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236
views
how shoud the phred score be intepreted?
sequencing
updated 1 day ago by 152k • written 1 day ago by ▴ 70
0
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3
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345
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Inherited pipeline uses RNA-seq variant calls for WASP filtering—shouldn’t it be external SNPs?
WASP
updated 1 day ago by 21k • written 4 days ago by ▴ 40
0
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0
replies
108
views
Identifying RBP motifs overlapping exons
motifs bedtools RBP
2 days ago by RK • 0
0
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0
replies
113
views
WGCNA analysis for Proteomics data
Proteomics WGCNA
2 days ago by Sumit Paliwal ▴ 40
3
votes
8
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6.6k
views
7 follow
Cellranger count pipestance failed: The read lengths are incompatible with all the chemistries
10x cellranger single-cell
updated 2 days ago by • 0 • written 3.0 years ago by ★ 1.7k
0
votes
1
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580
views
News: Hands-On Workshop - Next-Generation Sequencing Data Analysis: A Practical Introduction (September 10-12, 2025 in Berlin, Germany)
Workshop RNA-Seq Illumina VariantCalling DNA-Seq
2 days ago by ecSeq Bioinformatics ▴ 20
0
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0
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117
views
How to merge multiple pangenome graph files (generated by MC and PGGB)?
vg pangenome Minigraph-Cactus PGGB
2 days ago by Yao ▴ 30
1
vote
0
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181
views
Can iHS and XP-EHH be applied to targeted sequencing data?
sequencing targeted ngs ihs
3 days ago by slzr_ ▴ 10
1
vote
0
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192
views
Identify SNP, Indel variants from a List of FASTA sequence
SNP
4 days ago by Trinh ▴ 10
2
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3
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354
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PacBio amplicon reads partially aligned using minimap2 – library or analysis issue?
PacBio minimap2 alignment variants pbmm2
1 day ago by louisflower1999 • 0
0
votes
0
replies
621
views
Job: Biomedical Data Scientist / Systems Biologist / Omics Data Analyst / Bioinformatician / Computational Biologist (Tulane University, New Orleans, LA)
TUPulm
4 days ago by yzhou40 • 0
0
votes
0
replies
242
views
Batch effect in codominant microsatellite data – how to correct
population-genetics batch-effect R microsatellite genotyping
4 days ago by shervin • 0
2
votes
3
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374
views
UCSC genome browser negative strand positions
Genomic Data Browser UCSC Visualization Genome
updated 4 days ago by ★ 1.8k • written 5 days ago by ▴ 20
0
votes
1
reply
259
views
Error when computing bedtools bamtobed -bedpe
human bedtools libraries illumina bamtobed
updated 4 days ago by 88k • written 4 days ago by ▴ 10
0
votes
9
replies
775
views
Ligand-Receptor analysis using LIANA - question about specificity
scRNA-seq communication cell-cell
updated 5 days ago by ▴ 10 • written 8 days ago by ▴ 190
2
votes
4
replies
1.2k
views
PRS calculation from two sample genotype results
prs calculation
updated 5 days ago by ▴ 10 • written 6 months ago by • 0
1
vote
16
replies
6.0k
views
PRS in UK Biobank - no covariate file and no phenotype file
UK Biobank PRS
3.8 years ago by Jalil Sharif ▴ 80
40
votes
14
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2.6k
views
13 follow
Forum: How do you estimate time to complete a project or task?
career ngs
updated 5 days ago by • 0 • written 5 months ago by ▴ 990
0
votes
0
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197
views
News: Introduction to Deep Learning for Biologists - online course, 3–7 November
MachineLearning Python deepLearning ConvolutionalNeuralNetwork
5 days ago by Physalia-courses ★ 2.6k
1
vote
2
replies
827
views
Running trajectory and velocity analysis with multiple samples
seurat velocity loom trajectory
written 15 months ago by ▴ 70
2
votes
6
replies
565
views
Weird p-value distribution on edgeR results
edgeR pvalue-distribution gene-expression
updated 4 days ago by ★ 8.2k • written 5 days ago by ▴ 10
0
votes
1
reply
265
views
NMR modelling using xplor-NIH
peptide xplor-NIH NMR
4 days ago by npk107 • 0
1
vote
5
replies
398
views
PCA interpretation
chip seq PCA
updated 2 hours ago by 88k • written 5 days ago by • 0
0
votes
0
replies
226
views
News: course: Reproducibility in Bioinformatics - Only 2 seats remain!
Singularity Git Reproducibility Docker Snakemake
6 days ago by Physalia-courses ★ 2.6k
0
votes
0
replies
216
views
Annotate phylogenetic trees with bars or strips
otu phylogenetics R taxonomy metabarcoding
6 days ago by Luca Arbore ▴ 10
2
votes
2
replies
425
views
Identifying Long Reads Spanning Chromosomal Breakpoints
ONT samtools Whole-Genome
updated 6 days ago by ★ 2.0k • written 7 days ago by ▴ 10
0
votes
2
replies
353
views
PAML output
PAML Codeml Selection
updated 2 days ago by ★ 1.1k • written 6 days ago by • 0
1
vote
0
replies
276
views
how to produce your own Nx plot
R contiguity plot Nx
6 days ago by Matteo Ungaro ▴ 130
1
vote
2
replies
404
views
Interpreting inconsistency between BLAST hits and phylogenetic clustering i
tree phylogenetic blast
5 days ago by triplee0305 ▴ 20
0
votes
0
replies
244
views
News: Online course - Environmental Metagenomics - 13-17 October
Illumina MAGs Nanopore Metagenomics
6 days ago by Physalia-courses ★ 2.6k
0
votes
2
replies
371
views
Deg Difference in Deseq2
Deg
updated 6 days ago by 15k • written 6 days ago by • 0
0
votes
0
replies
287
views
No gene_trans_map file in CD-HIT-EST output
cd-hit-est Trinity RNAseq Trinotate
updated 6 days ago by 152k • written 6 days ago by • 0
0
votes
3
replies
436
views
MultiQC report - unique reads from sequence counts
fastQC unique reads multiQC
5 days ago by Rozita ▴ 40
2
votes
3
replies
411
views
NCBI Reference Genomes
genomes ncbi
updated 6 days ago by 152k • written 7 days ago by ▴ 70
0
votes
0
replies
269
views
GATK HaplotypeCaller missed variants in amplicon gene panel data
amplicon gene_panel haplotypecaller variant_calling gatk
7 days ago by Sofya • 0
121,532 results • Page 1 of 2431
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Comment: Trouble getting representatives from clustered_nr database
combining fasta files
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Comment: Missing gem_classification.csv in Cell Ranger 9.0.0 Output Using cellranger mult by tlallihuacan • 0
Thanks @genomax I did that the next day I saw I didn't get the answer here, I am coming back now. This is what 10x answered: "Thank yo…
Answer: quality control for 16s metagenome reads by Asaf 10k
I would have: 1. Discussed it with the sequencing service provider, there might be a problem with the machine (I've never seen such a pat…
Comment: PCA interpretation by ATpoint 88k
I do not recommend exploring noise-prone assays like ChIP-seq in a "blind" matter like this, using just the BAM files as input. Do proper p…
Comment: Loss of strandedness in the Illumina Strandedness Total RNA protocol by ATpoint 88k
No, I've never seen this before other than people used different kits than anticipated, or things were done wrong in the lab. Use an indepe…
Answer: Loss of strandedness in the Illumina Strandedness Total RNA protocol by Gordon Smyth ★ 8.2k
Running featureCounts would confirm for certain whether the RNA-seq is stranded or not, and also whether it appears usable or not. See: htt…
Comment: Which Reference Hg38 or T2T?? Both?? by Jon • 0
Those were BLAST results using the default NCBI Core_nt database, which apparently includes human reads sequenced nearly 20-25 years ago, s…
Comment: How to rank genes for GSEA using edgeR-LRT results ? by Gordon Smyth ★ 8.2k
Yes. That is a quasi t-statistic.
Comment: Problem with Mirdeep2 and Randfold output by Raquel • 0
Hi! I'm having the same problem. Did you solve it? Thank you, Best
Comment: Trouble getting representatives from clustered_nr database by GenoMax 152k
Will take a look at the script. In meantime, you can use `EntrezDirect` ([**LINK**][1]) to get the sequences. $ efetch -db protein -i…
Comment: Trouble getting representatives from clustered_nr database by Adolfo • 0
The script comes with `clustered_nr` database located [here][1]. And yes, it doesn't look like a valid genbank accession, however it exists…
Comment: Trouble getting representatives from clustered_nr database by GenoMax 152k
Which version of `blast+` are you using? I am not seeing this helper script with lastest `v.2.16.0`. > one accession returned from the sc…
Comment: Best Tool for Fast RNA-Seq Transcriptome Alignment to Extract Unmapped Reads by aeb ▴ 20
Hey @delaneyksull. Following up on this, it looks like kallisto has a `--fusion` option in older versions (before version 0.50.0). This loo…
Comment: TopHat installation error by david.leader • 0
This assumes that version 2 of python is installed on your machine and is aliased as python2. In my case a version was present (check with:…
Comment: Inherited pipeline uses RNA-seq variant calls for WASP filtering—shouldn’t it be by i.sudbery 21k
Its always unclear what to do for ASE/eQTL when you don't have matching DNAseq. Infact, you ideally want matched, phased, haplotypes! I th…
Comment: Which Reference Hg38 or T2T?? Both?? by GenoMax 152k
> but if I get 100% alignment with a couple mismatched bases at say 98-100% ID, those are the ones I'm looking at. It is not clear what da…
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