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121,515 results • Page
1 of 2431
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55
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Can iHS and XP-EHH be applied to targeted sequencing data?
sequencing
targeted
ngs
ihs
11 hours ago by
slzr_
• 0
0
votes
0
replies
54
views
Identify SNP, Indel variants from a List of FASTA sequence
SNP
13 hours ago by
Trinh
• 0
0
votes
1
reply
104
views
PacBio amplicon reads partially aligned using minimap2 – library or analysis issue?
PacBio
minimap2
alignment
variants
pbmm2
updated 8 hours ago by
GenoMax
152k • written 21 hours ago by
louisflower1999
• 0
842
votes
170
replies
181k
views
112 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 9 weeks ago by
Biostar
3.6k • written 8.6 years ago by
Istvan Albert
102k
0
votes
0
replies
166
views
Job:
Biomedical Data Scientist / Systems Biologist / Omics Data Analyst / Bioinformatician / Computational Biologist (Tulane University, New Orleans, LA)
TUPulm
1 day ago by
yzhou40
• 0
0
votes
0
replies
99
views
Inherited pipeline uses RNA-seq variant calls for WASP filtering—shouldn’t it be external SNPs?
WASP
1 day ago by
jonas.andersson
▴ 40
0
votes
0
replies
88
views
Batch effect in codominant microsatellite data – how to correct
population-genetics
batch-effect
R
microsatellite
genotyping
1 day ago by
shervin
• 0
2
votes
3
replies
230
views
UCSC genome browser negative strand positions
Genomic
Data
Browser
UCSC
Visualization
Genome
updated 1 day ago by
Maximilian Haeussler
★ 1.8k • written 2 days ago by
ijarne
▴ 20
0
votes
1
reply
126
views
Error when computing bedtools bamtobed -bedpe
human
bedtools
libraries
illumina
bamtobed
updated 1 day ago by
ATpoint
88k • written 1 day ago by
María José
▴ 10
0
votes
9
replies
566
views
Ligand-Receptor analysis using LIANA - question about specificity
scRNA-seq
communication
cell-cell
updated 1 day ago by
Muhammad
• 0 • written 5 days ago by
abedkurdi10
▴ 190
1
vote
4
replies
1.1k
views
PRS calculation from two sample genotype results
prs
calculation
updated 1 day ago by
Muhammad
• 0 • written 6 months ago by
Arun
• 0
1
vote
16
replies
5.9k
views
PRS in UK Biobank - no covariate file and no phenotype file
UK
Biobank
PRS
3.8 years ago by
Jalil Sharif
▴ 80
39
votes
14
replies
2.5k
views
13 follow
Forum:
How do you estimate time to complete a project or task?
career
ngs
updated 1 day ago by
Анна
• 0 • written 5 months ago by
sviatoslav.kendall
▴ 980
0
votes
0
replies
82
views
News:
Introduction to Deep Learning for Biologists - online course, 3–7 November
MachineLearning
Python
deepLearning
ConvolutionalNeuralNetwork
1 day ago by
Physalia-courses
★ 2.6k
1
vote
2
replies
723
views
Running trajectory and velocity analysis with multiple samples
seurat
velocity
loom
trajectory
written 15 months ago by
gogeni5529
▴ 70
0
votes
6
replies
359
views
Weird p-value distribution on edgeR results
edgeR
pvalue-distribution
gene-expression
updated 1 day ago by
Gordon Smyth
★ 8.2k • written 2 days ago by
Guillermo
• 0
0
votes
1
reply
138
views
NMR modelling using xplor-NIH
peptide
xplor-NIH
NMR
1 day ago by
npk107
• 0
1
vote
3
replies
210
views
PCA interpretation
chip
seq
PCA
updated 2 days ago by
rfran010
★ 1.6k • written 2 days ago by
Irving
• 0
0
votes
0
replies
115
views
News:
course: Reproducibility in Bioinformatics - Only 2 seats remain!
Singularity
Git
Reproducibility
Docker
Snakemake
2 days ago by
Physalia-courses
★ 2.6k
0
votes
0
replies
114
views
Annotate phylogenetic trees with bars or strips
otu
phylogenetics
R
taxonomy
metabarcoding
2 days ago by
Luca Arbore
▴ 10
2
votes
2
replies
311
views
Identifying Long Reads Spanning Chromosomal Breakpoints
ONT
samtools
Whole-Genome
updated 2 days ago by
trausch
★ 2.0k • written 4 days ago by
Noah
▴ 10
0
votes
1
reply
198
views
PAML output
PAML
Codeml
Selection
updated 2 days ago by
manaswwm
▴ 570 • written 3 days ago by
Morjina
• 0
1
vote
0
replies
172
views
how to produce your own Nx plot
R
contiguity
plot
Nx
3 days ago by
Matteo Ungaro
▴ 130
1
vote
2
replies
268
views
Interpreting inconsistency between BLAST hits and phylogenetic clustering i
tree
phylogenetic
blast
2 days ago by
triplee0305
▴ 20
0
votes
0
replies
140
views
News:
Online course - Environmental Metagenomics - 13-17 October
Illumina
MAGs
Nanopore
Metagenomics
3 days ago by
Physalia-courses
★ 2.6k
0
votes
2
replies
255
views
Deg Difference in Deseq2
Deg
updated 3 days ago by
swbarnes2
15k • written 3 days ago by
j.k.owaresat
• 0
0
votes
0
replies
185
views
No gene_trans_map file in CD-HIT-EST output
cd-hit-est
Trinity
RNAseq
Trinotate
updated 3 days ago by
GenoMax
152k • written 3 days ago by
ofarinas621
• 0
0
votes
3
replies
306
views
MultiQC report - unique reads from sequence counts
fastQC
unique
reads
multiQC
2 days ago by
Rozita
▴ 40
2
votes
3
replies
285
views
NCBI Reference Genomes
genomes
ncbi
updated 3 days ago by
GenoMax
152k • written 3 days ago by
anna
▴ 70
0
votes
0
replies
164
views
GATK HaplotypeCaller missed variants in amplicon gene panel data
amplicon
gene_panel
haplotypecaller
variant_calling
gatk
3 days ago by
Sofya
• 0
0
votes
1
reply
358
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 1 day ago by
GenoMax
152k • written 3 days ago by
tlallihuacan
• 0
0
votes
0
replies
150
views
Extracting logR and Baf files genome studio
Genomestudio
3 days ago by
1769mkc
★ 1.3k
0
votes
1
reply
321
views
Statistical analysis in a metagenomics study to validate biological differences
Metagenomics
analysis
updated 3 days ago by
chen
★ 2.5k • written 7 days ago by
Chijioke
• 0
1
vote
2
replies
516
views
Assembly issues
adapters
Assembly
Spades
updated 3 days ago by
chen
★ 2.5k • written 4 weeks ago by
anna
• 0
0
votes
5
replies
536
views
Trouble removing adapters from sequences using cutadapt
removal
cutadapt
adapter
primer
updated 3 days ago by
chen
★ 2.5k • written 9 days ago by
k.lagan
• 0
0
votes
5
replies
1.9k
views
Fastp
fastp
updated 3 days ago by
chen
★ 2.5k • written 3.2 years ago by
nishimalhotra2612
▴ 50
5
votes
10
replies
701
views
Need help using ExpansionHunter
ExpansionHunter
1 day ago by
brianhill_nc
• 0
0
votes
1
reply
216
views
How to extract gene list from GEO dataset in R
coding
beginner
question
r
updated 2 days ago by
manaswwm
▴ 570 • written 3 days ago by
decorus
• 0
0
votes
0
replies
195
views
WGBS Analysis with 1 control sample and 6 disease samples
one
WGBS
sample
4 days ago by
Cassandra
• 0
0
votes
0
replies
226
views
Comparing and plotting multinomial elastic net performance
ROC
elasticnet
plotting
glmnet
machinelearning
4 days ago by
bioinfo
• 0
2
votes
3
replies
363
views
How to add gene lable on GSEA plot
gseaplot
R
updated 3 days ago by
yura.grabovska
▴ 780 • written 4 days ago by
Emy Alade
▴ 20
0
votes
0
replies
227
views
Adding New Samples to Existing VCF Files graphtyper2
graphtyper2
existing_vcf
add_new_samples
4 days ago by
upadhyay.maulik
• 0
2
votes
5
replies
439
views
Seurat dims and QC questions
dims
updated 4 days ago by
1769mkc
★ 1.3k • written 4 days ago by
reddyornah
• 0
1
vote
1
reply
282
views
Duplication rate as reported by fastp.
fastp
duplication
RNA-seq
updated 4 days ago by
GenoMax
152k • written 5 days ago by
Anjan
▴ 840
0
votes
2
replies
568
views
Is it appropriate to include singleton reads with paired-end datasets for low-coverage Anaplasma marginale comparative genome analysis?
assembly
analysis
coverage
genome
singletons
comparative
updated 5 days ago by
Mensur Dlakic
★ 29k • written 5 days ago by
ashiqullah024
• 0
0
votes
1
reply
267
views
ComBat for Multiple Batch Effects in Methylation Data (Chip, Row, Plate)
ComBat
methylation
EPIC
batch-correction
updated 1 day ago by
Basti
★ 2.1k • written 5 days ago by
Eliveri
▴ 350
0
votes
1
reply
267
views
Using a Seurat object to create a cellchat object
cellchat
3 days ago by
m.sharghi
• 0
0
votes
0
replies
232
views
WGCNA - High R2 and Mean connectivity at low soft power
WGCNA
5 days ago by
Leonard Barnabas
• 0
0
votes
0
replies
211
views
How do I combine or integrate my VDJ data for TCR and BCR with seurat object?
VDJ
scRepertoire
Seurat
updated 5 days ago by
GenoMax
152k • written 5 days ago by
Jaber
▴ 30
0
votes
2
replies
405
views
DGE analysis in Seurat using paired samples per donor ?
paired
seurat
dge
sample
2 days ago by
Picasa
▴ 680
121,515 results • Page
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The Biostar Herald for Thursday, May 22, 2025
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DESeq2 analysis: huge number of outliers and refitting
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Answer: UCSC genome browser negative strand positions
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Comment: PacBio amplicon reads partially aligned using minimap2 – library or analysis iss
by
GenoMax
152k
Only including this as an alternate option to try (if your reads at HiFi) : https://github.com/PacificBiosciences/pbAA > but both the 5′ a…
Comment: NMR modelling using xplor-NIH
by
npk107
• 0
if anybody knows any good resources about how to explore nmr modelling using xplor-nih please let me know.
Comment: Missing gem_classification.csv in Cell Ranger 9.0.0 Output Using cellranger mult
by
GenoMax
152k
Reach out to 10x tech support since you have not received a response yet. They should provide an official answer, in case this output file …
Comment: Weird p-value distribution on edgeR results
by
Gordon Smyth
★ 8.2k
No outliers. Very clear hidden variable that hasn't been accounted for. voomLmFit will give same results here as edgeR.
Answer: UCSC genome browser negative strand positions
by
Maximilian Haeussler
★ 1.8k
I don't understand the question: this has nothing to do with the browser, right? You use a tool to transform coordinates and that tool give…
Answer: Error when computing bedtools bamtobed -bedpe
by
ATpoint
88k
Please read manuals of tools you use first. ```bash Tool: bedtools bamtobed (aka bamToBed) Version: v2.30.0 Summary: Converts BAM alig…
Answer: Ligand-Receptor analysis using LIANA - question about specificity
by
Muhammad
• 0
one potential reason for this could be the inherent sparsity of single-cell RNA-seq data. Single-cell RNA-seq often results in a relatively…
Comment: ComBat for Multiple Batch Effects in Methylation Data (Chip, Row, Plate)
by
Basti
★ 2.1k
It is generally better to include your batch effects in your model for differential analysis. Which tool will you use ? Usually, modelling …
Answer: PRS calculation from two sample genotype results
by
Muhammad
• 0
To calculate polygenic risk scores (PRS) from genotype results, especially for diseases like Cardiovascular or Pancreatic cancer without ph…
Comment: Weird p-value distribution on edgeR results
by
Guillermo
• 0
Hi Gordon! Thanks for answering. Originally I only performed PCA on the log2 CPM. I'm afraid I forgot to use the MDS plot to check the dis…
Answer: PRS in UK Biobank - no covariate file and no phenotype file
by
Muhammad
• 0
To generate a covariate file, you can use your UK Biobank metadata files. These files contain information about the samples, including sex …
Comment: Ligand-Receptor analysis using LIANA - question about specificity
by
abedkurdi10
▴ 190
Do you have any insights or ideas to take them into consideration?
Comment: Weird p-value distribution on edgeR results
by
Guillermo
• 0
Hi there! Thanks for answering. Yes, I kept performing PCA after each removal, looking for new outliers. The result was a never-ending pr…
Comment: Need help using ExpansionHunter
by
brianhill_nc
• 0
Thanks, I will work on that more soon. Someone said that you could simply count CAG repeats on the genome browser of Nebula from certain …
Comment: UCSC genome browser negative strand positions
by
rfran010
★ 1.6k
Would this be related to some function that takes the "end" as the start for negative strand features? E.g. Exon1: chr1 100 500 E…
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