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121,530 results • Page
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Votes
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0
votes
0
replies
28
views
Loss of strandedness in the Illumina Strandedness Total RNA protocol
Illumina
RNA-seq
reads
stranded
52 minutes ago by
Anjan
▴ 840
1
vote
2
replies
824
views
Problem with Mirdeep2 and Randfold output
mirdeep2
Randfold
updated 8 hours ago by
Raquel
• 0 • written 14 months ago by
otieno43
▴ 40
0
votes
0
replies
67
views
Help using ShinyCell2 and Seurat v5 object.
shinycell
seurat
shiny
shinycell2
scRNA
12 hours ago by
Jamie
• 0
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
Biostar
3.6k • written 8.6 years ago by
Istvan Albert
102k
0
votes
0
replies
59
views
News:
Machine Learning for Multi-Omics Integration at the University of Barcelona– Dec 2025
Machine-Learning
Sulti-Omics
Depp-Learning
Data-Integration
BigData
13 hours ago by
Physalia-courses
★ 2.6k
0
votes
0
replies
70
views
Compare alternative splicing patterns between human and mouse?
orthologs
rna-seq
splicing
alternative
14 hours ago by
aeb
▴ 20
2
votes
3
replies
147
views
Trouble getting representatives from clustered_nr database
database
blast
updated 8 hours ago by
GenoMax
152k • written 14 hours ago by
Adolfo
• 0
0
votes
0
replies
63
views
FindTransferAnchors (reference prediction) vs Manual Annotations
Seurat
15 hours ago by
reddyornah
• 0
0
votes
6
replies
258
views
Which Reference Hg38 or T2T?? Both??
Host
Removal
2 hours ago by
Jon
• 0
3
votes
4
replies
211
views
NCBI Datasets CLI Question
ncbi-datasets
1 day ago by
Bjorn
• 0
0
votes
0
replies
97
views
Incomplete assembly in HPRC dataset
pangenome
HPRC
reference
1 day ago by
ohell
• 0
3
votes
3
replies
221
views
Joint Calling for Large Germline WGS Cohort
NGS
RAM
cohort
Genomics
WGS
updated 1 day ago by
Jeremy Leipzig
23k • written 1 day ago by
j.k3096
▴ 20
0
votes
4
replies
226
views
how shoud the phred score be intepreted?
sequencing
updated 1 day ago by
GenoMax
152k • written 1 day ago by
QX
▴ 70
0
votes
3
replies
330
views
Inherited pipeline uses RNA-seq variant calls for WASP filtering—shouldn’t it be external SNPs?
WASP
updated 17 hours ago by
i.sudbery
21k • written 4 days ago by
jonas.andersson
▴ 40
0
votes
0
replies
97
views
Identifying RBP motifs overlapping exons
motifs
bedtools
RBP
1 day ago by
RK
• 0
0
votes
0
replies
103
views
WGCNA analysis for Proteomics data
Proteomics
WGCNA
1 day ago by
Sumit Paliwal
▴ 40
0
votes
0
replies
105
views
quality control for 16s metagenome reads
quality
metagneome
control
16s
fastp
1 day ago by
m90
▴ 30
3
votes
8
replies
6.6k
views
7 follow
Cellranger count pipestance failed: The read lengths are incompatible with all the chemistries
10x
cellranger
single-cell
updated 1 day ago by
zhang
• 0 • written 3.0 years ago by
firestar
★ 1.7k
0
votes
1
reply
569
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
1 day ago by
ecSeq Bioinformatics
▴ 20
0
votes
0
replies
110
views
How to merge multiple pangenome graph files (generated by MC and PGGB)?
vg
pangenome
Minigraph-Cactus
PGGB
1 day ago by
Yao
▴ 30
1
vote
0
replies
173
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
replies
184
views
Identify SNP, Indel variants from a List of FASTA sequence
SNP
3 days ago by
Trinh
▴ 10
2
votes
3
replies
347
views
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
563
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
232
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
replies
363
views
UCSC genome browser negative strand positions
Genomic
Data
Browser
UCSC
Visualization
Genome
updated 4 days ago by
Maximilian Haeussler
★ 1.8k • written 5 days ago by
ijarne
▴ 20
0
votes
1
reply
250
views
Error when computing bedtools bamtobed -bedpe
human
bedtools
libraries
illumina
bamtobed
updated 4 days ago by
ATpoint
88k • written 4 days ago by
María José
▴ 10
0
votes
9
replies
759
views
Ligand-Receptor analysis using LIANA - question about specificity
scRNA-seq
communication
cell-cell
updated 4 days ago by
Muhammad
▴ 10 • written 8 days ago by
abedkurdi10
▴ 190
2
votes
4
replies
1.2k
views
PRS calculation from two sample genotype results
prs
calculation
updated 4 days ago by
Muhammad
▴ 10 • written 6 months ago by
Arun
• 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
replies
2.6k
views
13 follow
Forum:
How do you estimate time to complete a project or task?
career
ngs
updated 4 days ago by
Анна
• 0 • written 5 months ago by
sviatoslav.kendall
▴ 990
0
votes
0
replies
188
views
News:
Introduction to Deep Learning for Biologists - online course, 3–7 November
MachineLearning
Python
deepLearning
ConvolutionalNeuralNetwork
4 days ago by
Physalia-courses
★ 2.6k
1
vote
2
replies
820
views
Running trajectory and velocity analysis with multiple samples
seurat
velocity
loom
trajectory
written 15 months ago by
gogeni5529
▴ 70
2
votes
6
replies
554
views
Weird p-value distribution on edgeR results
edgeR
pvalue-distribution
gene-expression
updated 4 days ago by
Gordon Smyth
★ 8.2k • written 5 days ago by
Guillermo
▴ 10
0
votes
1
reply
257
views
NMR modelling using xplor-NIH
peptide
xplor-NIH
NMR
4 days ago by
npk107
• 0
1
vote
4
replies
374
views
PCA interpretation
chip
seq
PCA
updated 1 day ago by
swbarnes2
15k • written 5 days ago by
Irving
• 0
0
votes
0
replies
218
views
News:
course: Reproducibility in Bioinformatics - Only 2 seats remain!
Singularity
Git
Reproducibility
Docker
Snakemake
5 days ago by
Physalia-courses
★ 2.6k
0
votes
0
replies
209
views
Annotate phylogenetic trees with bars or strips
otu
phylogenetics
R
taxonomy
metabarcoding
5 days ago by
Luca Arbore
▴ 10
2
votes
2
replies
414
views
Identifying Long Reads Spanning Chromosomal Breakpoints
ONT
samtools
Whole-Genome
updated 5 days ago by
trausch
★ 2.0k • written 7 days ago by
Noah
▴ 10
0
votes
2
replies
341
views
PAML output
PAML
Codeml
Selection
updated 2 days ago by
cfos4698
★ 1.1k • written 6 days ago by
Morjina
• 0
1
vote
0
replies
269
views
how to produce your own Nx plot
R
contiguity
plot
Nx
6 days ago by
Matteo Ungaro
▴ 130
1
vote
2
replies
395
views
Interpreting inconsistency between BLAST hits and phylogenetic clustering i
tree
phylogenetic
blast
5 days ago by
triplee0305
▴ 20
0
votes
0
replies
235
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
362
views
Deg Difference in Deseq2
Deg
updated 6 days ago by
swbarnes2
15k • written 6 days ago by
j.k.owaresat
• 0
0
votes
0
replies
278
views
No gene_trans_map file in CD-HIT-EST output
cd-hit-est
Trinity
RNAseq
Trinotate
updated 6 days ago by
GenoMax
152k • written 6 days ago by
ofarinas621
• 0
0
votes
3
replies
426
views
MultiQC report - unique reads from sequence counts
fastQC
unique
reads
multiQC
5 days ago by
Rozita
▴ 40
2
votes
3
replies
401
views
NCBI Reference Genomes
genomes
ncbi
updated 6 days ago by
GenoMax
152k • written 6 days ago by
anna
▴ 70
0
votes
0
replies
261
views
GATK HaplotypeCaller missed variants in amplicon gene panel data
amplicon
gene_panel
haplotypecaller
variant_calling
gatk
6 days ago by
Sofya
• 0
0
votes
1
reply
552
views
Missing gem_classification.csv in Cell Ranger 9.0.0 Output Using cellranger multi with Combined Human-Mouse Reference
gem_classification
10x
cellranger_multi
combined_human-mouse_reference
updated 4 days ago by
GenoMax
152k • written 6 days ago by
tlallihuacan
• 0
0
votes
0
replies
248
views
Extracting logR and Baf files genome studio
Genomestudio
6 days ago by
1769mkc
★ 1.3k
121,530 results • Page
1 of 2431
Recent Votes
Comment: Trouble getting representatives from clustered_nr database
A: Difference between primary nad capture targets
Comment: Trouble getting representatives from clustered_nr database
combining fasta files
Answer: combining fasta files
Answer: Samfiles
How do you estimate time to complete a project or task?
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Recent Replies
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…
Comment: Which Reference Hg38 or T2T?? Both??
by
GenoMax
152k
> I have assembled some of them with metaspades which gave me good contigs in the 4000bp that blast identified at 100%, so my ASSUMPTION i…
Comment: How to rank genes for GSEA using edgeR-LRT results ?
by
Picasa
▴ 680
If I am using edgeR QLF, can I use the F column for the z calcul? z <- sign(QLF$table$logFC) * sqrt(QLF$table$F)
Comment: Which Reference Hg38 or T2T?? Both??
by
Jon
• 0
![enter image description here][1] [1]: /media/images/7880cb6b-9bae-4506-8f27-380a5515 This is one of the examples I'm talking about. …
Comment: Which Reference Hg38 or T2T?? Both??
by
Jon
• 0
The reference I'm having issues is the Naegleria Fowleri Karachi NF001, as this is the one that shows up in my samples. Everything I have …
Answer: Which Reference Hg38 or T2T?? Both??
by
GenoMax
152k
> So if I have my human sample and remove reads matching T2T, that Should? give me a host free set of reads??? For purpose of host deconta…
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