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120,439 results • Page
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0
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9
views
Mapping OMIM IDs (for diseases) to MeSH IDs
phenotype
ontology
DISEASE
MESH
OMIM
41 minutes ago by
singhankit973
• 0
0
votes
2
replies
938
views
Gini Coefficient and Lorenz curve to measure uniformity of coverage
gini
lorenz curve
coverage uniformity
1 hour ago by
am
▴ 60
0
votes
6
replies
145
views
DESeq2 for multiple groups
usegalaxy
Limma
voom
Deseq2
2 hours ago by
banaalkhayrat123
• 0
1
vote
2
replies
293
views
Bowtie index size / richness matters ?
bowtie
5 hours ago by
maschi88
• 0
0
votes
1
reply
88
views
How to predict targets of miRNAs with indels in the seed region?
seed
indels
targets
miRNA
updated 6 hours ago by
i.sudbery
21k • written 14 hours ago by
jhonatan.henrique
• 0
828
votes
169
replies
167k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 5 months ago by
Biostar
3.4k • written 8.2 years ago by
Istvan Albert
102k
0
votes
0
replies
39
views
Full-length LINE1 for mm10
LTR
updated 2 hours ago by
GenoMax
149k • written 6 hours ago by
Bioinformatics_16
• 0
0
votes
1
reply
85
views
Limma Voom
Differential
analysis
updated 6 hours ago by
ATpoint
86k • written 8 hours ago by
maryak
▴ 20
0
votes
0
replies
29
views
Blog:
Novogene Single-cell and Spatial Multi-omics Case Study: Application in Bone Regeneration
Multi-omics
Single-cell
7 hours ago by
Novogene
▴ 460
0
votes
1
reply
71
views
SNP density visualization with circos in galaxy
visualization
CIRCOS
updated 8 hours ago by
Pierre Lindenbaum
165k • written 9 hours ago by
ag18090
• 0
0
votes
1
reply
105
views
Unusual File Count in 10x scMultiome Data for Cell Ranger ARC Processing
scMultiome
10x
fastq
human_cell_atlas
cellranger_arc
updated 12 hours ago by
GenoMax
149k • written 19 hours ago by
Wu-Sheng Zhang
• 0
0
votes
2
replies
128
views
How to determine new bacterial species from custom isolate?
species
genome
submission
updated 2 hours ago by
michael.ante
★ 3.9k • written 1 day ago by
marongiu.luigi
▴ 730
0
votes
1
reply
137
views
I want to merge 123 seurat objects in R, I am running into issues with memory, how do I do this/
seurat
merge
cell
single
updated 19 hours ago by
ATpoint
86k • written 23 hours ago by
biotrekker
▴ 110
0
votes
0
replies
81
views
News:
Online Course: Network Analysis in R (May 5-8)
R
NetworkAnalyis
Tidyverse
1 day ago by
Physalia-courses
★ 2.6k
0
votes
1
reply
130
views
News:
Short Survey on Genomic Data Management & Analysis Workflows
Analysis
Genomics
updated 18 hours ago by
Jeremy Leipzig
23k • written 1 day ago by
QMS
• 0
0
votes
1
reply
116
views
Motif enrichment across super-enhancer regions
motif
HOMER
enrichment
updated 1 day ago by
rfran010
★ 1.3k • written 1 day ago by
SEJAL
• 0
0
votes
0
replies
93
views
JASPAR Database
JASPAR
HOMER
1 day ago by
SEJAL
• 0
1
vote
3
replies
200
views
Finding ORFs in a FASTA file
MatrixScore
ORFs
Motifs
MotifScoring
Bioinformatics
updated 5 hours ago by
Michael
55k • written 1 day ago by
Melissa
• 0
1
vote
1
reply
123
views
How to perform Linkage Disequilibrium (LD) analysis in INDELS
SNPs
PLINK
linkage
disequilibrium
haploview
updated 11 minutes ago by
dthorbur
★ 2.8k • written 1 day ago by
Ant
▴ 40
0
votes
0
replies
113
views
Spatt2.1 a mirMap dependency, anyone know where I can get it?
miRmap
dependency
tarball
1 day ago by
RNAseqer
▴ 280
0
votes
0
replies
112
views
DeChat Nanopore read correction with Medaka correction?
ont
medaka
wgs
dechat
nanopore
1 day ago by
Mark
▴ 30
0
votes
0
replies
139
views
Why are phenotype values missing in PLINK analysis despite no NA values in the input?
PLINK
PRS
PHS
PGS
SNPanalysis
2 days ago by
comu
• 0
2
votes
2
replies
284
views
Should I not have any adapters after trimming?
RNA-seq
updated 2 days ago by
swbarnes2
14k • written 3 days ago by
bioinfo
▴ 150
1
vote
3
replies
300
views
Multiple fail points in fastqc file
fastqc
report
updated 2 days ago by
swbarnes2
14k • written 3 days ago by
dr.deepakkukkar
• 0
2
votes
5
replies
339
views
Incorrect gene naming (SYMBOL)
Gene-annotation
6 hours ago by
Biomed-jeh
▴ 70
0
votes
0
replies
182
views
Interactive UMAP for scRNA-seq Data
HTML
RMarkdown
Interactive-UMAP
scRNA-seq
updated 2 days ago by
Ram
44k • written 2 days ago by
s
• 0
1
vote
1
reply
252
views
Problem after subset of single cell integrated dataset in seurat using sctransform
seurat
integration
scRNAseq
sctransform
subset
3 days ago by
NGS_enthusiast
• 0
3
votes
4
replies
356
views
Per Sequence GC Content fail
fastqc
updated 3 days ago by
GenoMax
149k • written 3 days ago by
Eduardo
• 0
2
votes
5
replies
1.0k
views
Compare genomes of different species and published studies (different years, sequencing technologies...) is correct?
comparative-genomics
updated 5 hours ago by
dthorbur
★ 2.8k • written 3 days ago by
Bruno Santos
• 0
3
votes
3
replies
371
views
Why do people say it doesn't matter whether you run unassembled or assembled reads through Kraken?
assembly
unassembled-reads
Kraken
updated 5 hours ago by
dthorbur
★ 2.8k • written 3 days ago by
trkfs
▴ 10
3
votes
5
replies
312
views
Best way to provide sequences to Local Colabfold to not overload their mmseq2 server
Local
ColabFold
updated 3 days ago by
dthorbur
★ 2.8k • written 3 days ago by
myoui3122010
▴ 30
4
votes
9
replies
508
views
Preventing Conda/Mamba from accessing Anaconda repos when institution blocks them
conda
mamba
repos
miniforge
channels
updated 2 days ago by
Jesse
▴ 850 • written 3 days ago by
kalavattam
▴ 310
3
votes
6
replies
968
views
Tool:
A c library for reading and writing sequences in fasta and fastq format.
seqio
3 days ago by
dwpeng
▴ 110
0
votes
0
replies
173
views
Difference between mutect2 and strelka2
mutect2
strelka2
3 days ago by
ramiro.barrantes
▴ 20
0
votes
1
reply
293
views
GO Analysis Combine or Separate DEGs
clusterProfiler
GO
updated 3 days ago by
mark.ziemann
★ 2.0k • written 5 days ago by
Koki
• 0
1
vote
1
reply
351
views
scType on Xenium Spatial Transcriptomics
Spatial
Xenium
scType
updated 3 days ago by
geno89
▴ 10 • written 17 days ago by
Emma Jayne
▴ 10
0
votes
0
replies
173
views
How to extract the components of a cluster after pheatmap
Heatmap
Export
Cluster
3 days ago by
Luiza
• 0
0
votes
1
reply
473
views
Interpretation of MSMC2/PSMC/betaPSMC/ngsPSMC
Demography
PSMC
MSMC
updated 3 days ago by
csarabia
• 0 • written 3 months ago by
vap768
• 0
0
votes
3
replies
278
views
Metagenomic binnig step
binnig
tools
Metagenomics
updated 3 days ago by
Mensur Dlakic
★ 28k • written 4 days ago by
m90
▴ 30
0
votes
1
reply
224
views
Tool to phase genotyped large SV from short-read data?
sv
structural
variant
short-reads
haplotype
phasing
updated 3 days ago by
Pierre Lindenbaum
165k • written 3 days ago by
afurches
• 0
0
votes
0
replies
160
views
Normalisation for sample splice junction profiles
splicing
normalisation
RNAseq
3 days ago by
coolmattmonkey
• 0
0
votes
0
replies
164
views
Calculate base pair probability differences between Wild type and mutant sequences
probabilities
rnaplfold
rnafold
basepair
3 days ago by
RK
• 0
0
votes
1
reply
319
views
What is indicated by the red dotted lines in the `tiny_10x_pbmc.pdf` out put from `cellbender remove-background`
remove-background
cellbender
updated 3 days ago by
Bastien Hervé
6.1k • written 3 days ago by
joshua.theisen
▴ 30
1
vote
2
replies
321
views
Parameters for annotation with maker
Maker
masking
plant
annotation
2 days ago by
san96
▴ 170
5
votes
3
replies
279
views
Extracting Sequences from a FASTA File Using Exon Coordinates from a GTF File
gtf
fasta
updated 3 days ago by
colindaven
7.1k • written 4 days ago by
Milica
• 0
0
votes
2
replies
234
views
Low Read Mapping for Differentially Expressed Genes in 3' RNA-seq Analysis
gene-expression
single-end
RNA-seq
updated 3 days ago by
Ram
44k • written 4 days ago by
Emy Alade
• 0
2
votes
3
replies
260
views
mapDamage error
mapDamage
1000genomes
4 days ago by
anna.utili
• 0
0
votes
0
replies
175
views
News:
Online Course: Flow Cytometry Data Analysis with R/Bioconductor (17–20 March 2025)
R
Bioconductor
Flow-Cytometry
Cancer-Genomics
4 days ago by
Physalia-courses
★ 2.6k
2
votes
1
reply
230
views
Average length of mRNA on NCBI annotation seems too high
mRNA
updated 4 days ago by
lieven.sterck
15k • written 4 days ago by
yh1126
• 0
0
votes
0
replies
176
views
How to normalize qPCR results for covariates like cell type markers
Normalization
qPCR
RNA-Seq
4 days ago by
Sara
▴ 40
120,439 results • Page
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Comment: BLAST options: max_target_seqs and num_alignments
Comment: Installing VEP for a Specific Chromosome (e.g., Chromosome 1) is not possible??
Looking for a tool which provides mapping quality score distributions from BAM files
Looking for a tool which provides mapping quality score distributions from BAM files
Answer: Bowtie index size / richness matters ?
Comment: Finding ORFs in a FASTA file
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Recent Replies
Comment: How to perform Linkage Disequilibrium (LD) analysis in INDELS
by
dthorbur
★ 2.8k
Is there any way you can phase the data? And do you have access to the original VCF files with the data? All the tools I can think of start…
Answer: Gini Coefficient and Lorenz curve to measure uniformity of coverage
by
am
▴ 60
Hi Federico, I kept using ineq or python code: https://github.com/auroramaurizio/my_DNA_seq_pipelines/blob/main/GINI_index/Snakefile. I a…
Comment: DESeq2 for multiple groups
by
banaalkhayrat123
• 0
Yes Thank you!
Answer: Gini Coefficient and Lorenz curve to measure uniformity of coverage
by
abascalfederico
★ 1.2k
Hi, did you find a program to do this?
Comment: DESeq2 for multiple groups
by
GenoMax
149k
https://help.galaxyproject.org/c/usegalaxy-eu-support/6 is the forum for Galaxy EU Support.
Comment: How to determine new bacterial species from custom isolate?
by
michael.ante
★ 3.9k
Different species have different inherent mutation rates; check if your species of interest has some published values and compute if your i…
Comment: DESeq2 for multiple groups
by
ATpoint
86k
This you have to ask at the Galaxy support, they have a forum like this one here afaik.
Comment: DESeq2 for multiple groups
by
banaalkhayrat123
• 0
Thank you so much @ATpoint. That is amazing since I will try to run the analysis in RStudio. However, my question was namely in usegalaxy.e…
Comment: DESeq2 for multiple groups
by
banaalkhayrat123
• 0
Thank you so much @ATpoint. That is amazing since I will try to run the analysis in RStudio. However, my question was namely in usegalaxy.e…
Answer: DESeq2 for multiple groups
by
ATpoint
86k
For the first question: In DESeq2 ***I think*** you need to use a list with the `contrast` argument in `results()` to test fold changes of …
Comment: Compare genomes of different species and published studies (different years, seq
by
dthorbur
★ 2.8k
There are a lot of things to unpack here. But I would say the best course of action is to find genomic studies that do similar things with …
Comment: Why do people say it doesn't matter whether you run unassembled or assembled rea
by
dthorbur
★ 2.8k
What do you intend to use it for? For me, I use it for contamination quantification and removal. But there are plenty of use cases for usin…
Comment: Bowtie index size / richness matters ?
by
maschi88
• 0
I see, thank you. I'll change my code and build several indexes then.
Answer: How to predict targets of miRNAs with indels in the seed region?
by
i.sudbery
21k
The first thing to check is whether the sequence will still generate a valid miRNA molecule. The sequence of the pre-miRNA most form a hair…
Comment: Finding ORFs in a FASTA file
by
Michael
55k
Good point with the reverse strand, it isn't clear from the questions if scanning the reverse strand was part of the task. The comment on t…
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