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121,369 results • Page
1 of 2428
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0
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32
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Tutorial:
How to calculate partial correlation controlling cancer types
CRISPR
biology
correlation
computational
bioinformatics
2 hours ago by
Ming Tommy Tang
★ 4.6k
0
votes
1
reply
76
views
SAIGE-GENE error
R
SAIGE
updated 8 hours ago by
GenoMax
151k • written 9 hours ago by
smyiz
▴ 30
2
votes
1
reply
153
views
IGV track display problem: interval rectangle from BED file appears above all tracks in white, overlapping each other
IGV
bed
10 hours ago by
mcsimenc
▴ 30
1
vote
1
reply
86
views
Y-axis break in Volcano Plot
Volcano_Plot
Enhanced_Volcano
updated 12 hours ago by
GenoMax
151k • written 12 hours ago by
rajdeepboral00
▴ 70
839
votes
170
replies
179k
views
112 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 6 weeks ago by
Biostar
3.6k • written 8.5 years ago by
Istvan Albert
102k
1
vote
0
replies
68
views
How to rank a gene list using correlation coefficient and p-values for GSEA/clusterProfiler?
ClusterProfiler
GSEA
correlation
rank
genelist
14 hours ago by
c-wes
▴ 10
2
votes
4
replies
210
views
Nanopore data analysis
nanopore
updated 14 hours ago by
colindaven
7.6k • written 19 hours ago by
sarahmanderni
▴ 130
5
votes
2
replies
1.4k
views
What is the difference between norm --multiallelics -any versus --atomize?
bcftools
updated 14 hours ago by
ashotmarg2004
▴ 130 • written 21 months ago by
a615ebfb
▴ 50
0
votes
1
reply
102
views
checking the sequences that share origin
sequencing
updated 15 hours ago by
GenoMax
151k • written 15 hours ago by
QX
▴ 70
0
votes
0
replies
74
views
News:
Assembling Genomes with Oxford Nanopore: A Hands-On Guide to Long-Read Sequencing
Nanopore
GenomeAssembly
longreads
20 hours ago by
Physalia-courses
★ 2.6k
0
votes
2
replies
154
views
Bambu on illumina short reads sequencing
Bambu
updated 15 hours ago by
Rob
7.1k • written 20 hours ago by
Simone
• 0
0
votes
0
replies
89
views
Isoquant Major Exon Elongation
isoquant
nanopore
exon
1 day ago by
aico
• 0
0
votes
0
replies
97
views
bcftools run-roh error
roh
bcftools
updated 1 day ago by
GenoMax
151k • written 1 day ago by
Pratiksha
• 0
0
votes
0
replies
105
views
News:
Workshop: Virtual Single-Cell Transcriptomics, June 24–26
Transcriptomics
workshop
UConn
1 day ago by
zsc25001
▴ 10
1
vote
6
replies
266
views
How can I find KO IDs for ORF sequences from kofam_scan ?
biology
Computational
Bioinformatics
1 day ago by
Nikesh
• 0
0
votes
0
replies
110
views
VEP all genes are skipped due to invalid types
variants
GTF
VEP
annotation
1 day ago by
Titus
▴ 910
4
votes
3
replies
242
views
Isoform analysis after quantification with Salmon/Star
STAR
Salmon
Isoform
analysis
12 hours ago by
rajdeepboral00
▴ 70
0
votes
0
replies
97
views
Confidence in CIBERSORT (LM22) Deconvolution Output for Rare Cell Types — Best Practices?
LM22
DECONVOLUTION
CIBERSORT
1 day ago by
Pumla
• 0
1
vote
7
replies
319
views
Significant reads loss after fastp
fastp
loss
reads
updated 16 hours ago by
GenoMax
151k • written 1 day ago by
SpliceAndScript
• 0
1
vote
1
reply
166
views
Shinyapps Server Down?
Shinyapps
Posit
updated 1 day ago by
GenoMax
151k • written 1 day ago by
Arup Ghosh
3.3k
0
votes
2
replies
217
views
Data of microarray
Microarray
1 day ago by
Peter
• 0
0
votes
0
replies
136
views
How to run GSVA on scRNA-Seq analysis on multiple clusters and groups to compare per tumor sample?
GSVA
scRNA-Seq
1 day ago by
Minh-Anh
▴ 10
2
votes
4
replies
301
views
Best Tool for Fast RNA-Seq Transcriptome Alignment to Extract Unmapped Reads
mapping
rna-seq
1 day ago by
aeb
▴ 20
0
votes
2
replies
219
views
Time scaled tree with IQTree giving off looking branch length
bacteria
phylogeny
time
evolution
scaled
1 day ago by
SushiRoll
▴ 140
1
vote
2
replies
239
views
Signature Matrix Modifications/Subclustering
signature
matrix
scRNA-seq
seurat
cibersortx
2 days ago by
MitchT
▴ 10
4
votes
2
replies
228
views
Picard CollectRawWgsMetrics runs much slower on non-Apple chip machine
picard
updated 2 days ago by
Michael
55k • written 2 days ago by
adixon3
• 0
0
votes
0
replies
151
views
Reporting Imputed SNPs in GWAS
impute
GWAS
updated 2 days ago by
Ram
45k • written 2 days ago by
Aastha
• 0
0
votes
0
replies
131
views
Does Beagle use the reference genome for both phasing AND imputing genotypes?
beagle
genotypes
phasing
imputation
2 days ago by
giulia.trauzzi
▴ 30
0
votes
0
replies
131
views
In GERPplusplus, odd gerpelem outputs
GERP
evolutionary
gerpcol
substitution
gerpelem
rates
rejected
2 days ago by
Begonia_pavonina
▴ 210
6
votes
2
replies
236
views
required annotations for VQSR
VQSR
vcf
annotation
2 days ago by
Mahdi&Christ
▴ 20
4
votes
4
replies
346
views
Identify transgene insert loci/copy number in nanopore De-novo assembly
ont
nanopore
transgene
sequencing
wgs
2 days ago by
ctmfarland
▴ 20
9
votes
9
replies
525
views
Heatmap for visualizing the differentially expressed genes in RNA-seq data
R
DEseq2
RNA-seq
differentially-expressed
heatmap
2 days ago by
KABILAN
▴ 130
0
votes
1
reply
213
views
single-cell differential expression of unbalanced cell number
Seurat
scRNA-seq
updated 2 days ago by
ATpoint
88k • written 3 days ago by
Yingying
▴ 10
0
votes
1
reply
734
views
Differential Expression tests for cell-type clusters from a single-cell RNAseq dataset with no biological replicates
cell-type
DEG
DE
single-cell
updated 3 days ago by
Yingying
▴ 10 • written 5 months ago by
aa23871x
• 0
2
votes
10
replies
503
views
Annotation Issue using miRBASE gff
NGS
miRNA
updated 2 days ago by
GenoMax
151k • written 3 days ago by
anthony.santana.703.j
▴ 30
0
votes
0
replies
167
views
News:
Evo 2 webinar - 1 day left to register
AI.LLM.Biology.Genomics
3 days ago by
Claire Watson
▴ 60
1
vote
6
replies
352
views
Error Scaffolding with RagTag
scaffold
RagTag
updated 2 days ago by
Michael
55k • written 3 days ago by
Bipin
▴ 10
4
votes
0
replies
192
views
Tool:
biothings-mcp - MCP server to query genes, variants, chemicals, taxons
API
biothings
genes
AI
MCP
3 days ago by
Anton
▴ 100
2
votes
0
replies
170
views
Tool:
synergy-age-mcp - a database of synergistic and antagonistic genetic interactions in longevity
combination
longevity
MCP
ageing
3 days ago by
Anton
▴ 100
2
votes
0
replies
187
views
Tool:
opengenes-mcp - MCP server on the database for longevity genes
genes
databases
bioinformatics
longevity
MCP
3 days ago by
Anton
▴ 100
2
votes
0
replies
194
views
Tool:
gget-mcp - a bioinformatics toolkit for genomics queries and analysis (based on gget lbrary)
bioinformatics
libraries
MCP
AI
3 days ago by
Anton
▴ 100
0
votes
2
replies
228
views
Best pairwise alignment for insertion and deletion-containing sequences
sequence
python
biopython
pairwise
alignment
3 days ago by
rbpdee
▴ 50
2
votes
7
replies
452
views
How to deal with intermediate files
procedures
data
operations
updated 3 days ago by
GenoMax
151k • written 4 days ago by
ramiro.barrantes
▴ 60
1
vote
1
reply
209
views
Quality control metrics in mmCIF
PDB
protein
mmCIF
updated 3 days ago by
dthorbur
★ 3.0k • written 3 days ago by
Adrian
• 0
0
votes
1
reply
205
views
phage sequence no alignment to genome
prophage
bwa
phage
genome
alignment
updated 3 days ago by
GenoMax
151k • written 3 days ago by
Luwell
• 0
0
votes
1
reply
210
views
Mitochondrial Annotation Tool
Illumina
Bovine
Mitochondria
updated 3 days ago by
patrickdm
▴ 260 • written 3 days ago by
adarsh
▴ 60
1
vote
1
reply
251
views
Assessing the difference between a de novo assembly and a reference genome
hifiasm
MUMmmer
dnadiff
updated 3 days ago by
patrickdm
▴ 260 • written 4 days ago by
andrea
• 0
1
vote
1
reply
241
views
HISAT2 or STAR
alignment
hisat2
star
updated 3 days ago by
rfran010
★ 1.5k • written 3 days ago by
SpliceAndScript
• 0
0
votes
2
replies
244
views
What to do after fastp?
rna-seq
fastp
alignment
updated 3 days ago by
dthorbur
★ 3.0k • written 3 days ago by
SpliceAndScript
• 0
1
vote
1
reply
363
views
SNP calling from multiple genomes: No valid SNPs
samtools
bcftools
snp
plink
wgs
updated 4 days ago by
colindaven
7.6k • written 7 days ago by
emil.paulitz
• 0
121,369 results • Page
1 of 2428
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Answer: Isoform analysis after quantification with Salmon/Star
Answer: IGV track display problem: interval rectangle from BED file appears above all tr
A: R: Plotting MSMC/PSMC results using ggplot2
Answer: required annotations for VQSR
Comment: Phased haplotype using WGS data from Nebula Genomics and GATK
Answer: IGV track display problem: interval rectangle from BED file appears above all tr
How to rank a gene list using correlation coefficient and p-values for GSEA/clusterProfiler?
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Recent Replies
Comment: Trouble building combined pangenome graph with circularized genomes + embedded O
by
Jordan M Eizenga
▴ 740
That error is caused by a simple failure to open that file (which is created in the `vg prune`). Usually, that results from a typo in the f…
Comment: SAIGE-GENE error
by
GenoMax
151k
Segfaults are related to memory, which is what part of the message is telling you. If you are running this job under a job scheduler make s…
Answer: IGV track display problem: interval rectangle from BED file appears above all tr
by
mcsimenc
▴ 30
The problem was the filename suffix, it's meaningful in how IGV treats the file. It is .pk here, but changed to .bed and it works.
Comment: Y-axis break in Volcano Plot
by
GenoMax
151k
> Any help is appreciated You should consider upvoting and validating (accepting, green check mark) comments/answers you have received on …
Comment: Isoform analysis after quantification with Salmon/Star
by
rajdeepboral00
▴ 70
Thank you for your detailed reply
Answer: Nanopore data analysis
by
colindaven
7.6k
- Merge bams - yes. (why do you have so many ?). Merging fastqs before creating bams is easier (cat *.fastq.gz ) than bam merging. - 150…
Answer: What is the difference between norm --multiallelics -any versus --atomize?
by
ashotmarg2004
▴ 130
There is a related discussion here: https://github.com/samtools/bcftools/issues/2142
Answer: checking the sequences that share origin
by
GenoMax
151k
Without the presence of [**UMI**][1] in data, it would be difficult to say with certainty that a pair of sequences share an identical origi…
Comment: Bambu on illumina short reads sequencing
by
Rob
7.1k
I'll agree with GenoMax here. While the approach of bambu shares several methodological underpinnings with methods used for short-read qua…
Comment: Nanopore data analysis
by
GenoMax
151k
Data volume is going to depend on the amount of sequencing. Was this a PromethION flowcell? Tool should handle the data as long as you have…
Comment: Bambu on illumina short reads sequencing
by
GenoMax
151k
Did you see a recent thread --> https://www.biostars.org/p/9612865/ which delineates standard methods for short-read data. Bambu is meant…
Comment: Nanopore data analysis
by
sarahmanderni
▴ 130
The overall size for all bam files is around 150 GB. Is this common for nanopore and does this tools handle this volume of data? Thanks fo…
Comment: Nanopore data analysis
by
GenoMax
151k
How about using `modkit` provided by Nanopore for methylation data analysis: https://github.com/nanoporetech/modkit
Comment: Significant reads loss after fastp
by
GenoMax
151k
Will refer you back to my comment above. Don't be fixated on the Q scores. You don't say what kind of data this is but it may still align f…
Comment: Better splitting of mutliallelic sites then bcftools norm --m-any
by
gernophil
▴ 130
Because this question just received an upvote: I used `vt decompose -s` back in the days, but I think bcftools now also makes you choose th…
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