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1,000 results • Page
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News:
Online course: Meta-analysis in R
MetaAnalysis
Statistics
R
14 minutes ago by
carlopecoraro2
★ 2.5k
0
votes
9
replies
285
views
How can I retrieve wheat lysine non-acetylated sequences from the UniProt database?
UniProt
updated just now by
Elisabeth Gasteiger
★ 2.3k • written 4 hours ago by
Jacky
• 0
795
votes
167
replies
141k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 12 weeks ago by
Biostar
2.6k • written 7.4 years ago by
Istvan Albert
100k
0
votes
1
reply
59
views
10x VDJ (TCR/BCR) BAM to fastq
TCR
VDJ
BCR
10x
updated 54 minutes ago by
GenoMax
141k • written 2 hours ago by
predeus
★ 1.9k
0
votes
1
reply
65
views
DEseq2
RNA
DESeq2
seq
updated 1 hour ago by
ATpoint
81k • written 3 hours ago by
rrehimi
• 0
0
votes
0
replies
19
views
News:
Course - Agent-Based Modelling Using NetLogo - University of Lodz, Poland
Netlogo
IndividualBasedModels
AgentBasedModels
1 hour ago by
carlopecoraro2
★ 2.5k
4
votes
2
replies
115
views
Assume "yes" as the answer to any prompts with bioconda
docker
container
bioconda
updated 1 hour ago by
Juke34
8.5k • written 2 hours ago by
njornet
▴ 20
0
votes
0
replies
33
views
Tutorial:
DNA Methylation: Sequencing Techniques
WGBS
RRBS
2 hours ago by
Novogene
▴ 410
0
votes
1
reply
327
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
tree
phylogenetic
summarized
microbiome
updated 3 hours ago by
Akshay
• 0 • written 19 months ago by
Muhammad
• 0
0
votes
2
replies
127
views
Korean human genome reference file
GWAS
reference
imputation
updated 44 minutes ago by
GenoMax
141k • written 4 hours ago by
SeoGyun
• 0
1
vote
4
replies
196
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
updated 48 minutes ago by
GenoMax
141k • written 4 hours ago by
n_navy
• 0
0
votes
2
replies
157
views
RNA seq differential expression analysis
Regarding
seq
data
normalization
RNA
3 hours ago by
rrehimi
• 0
0
votes
1
reply
72
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
updated 30 minutes ago by
GenoMax
141k • written 4 hours ago by
kirillkirilenko
▴ 20
0
votes
0
replies
49
views
How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau
score
tspex
5 hours ago by
bioinfo223
▴ 10
0
votes
0
replies
58
views
How to root an unrooted tree with a known root tree?
phylogenetics
rooting
R
5 hours ago by
P.
• 0
0
votes
0
replies
63
views
Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
snpEff
7 hours ago by
ekirsch
• 0
0
votes
0
replies
88
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
11 hours ago by
renan.igor
• 0
1
vote
1
reply
155
views
Pediococcus acidilactici sequence analysis
BLAST
Gene-Ontology
updated 8 hours ago by
Ram
43k • written 14 hours ago by
anasjamshed
▴ 120
3
votes
1
reply
528
views
What is the normalization status of metabric data?
metabric
normalization
microarray
cbioportal
updated 13 hours ago by
etiennedanis
▴ 20 • written 19 months ago by
DareDevil
★ 4.3k
0
votes
0
replies
81
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
13 hours ago by
synat.keam
▴ 100
0
votes
1
reply
170
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 15 hours ago by
GenoMax
141k • written 16 hours ago by
ycts
• 0
2
votes
3
replies
366
views
DEG analysis of RNA-seq data across multiple tissues and two conditions
RNA-seq
EdgeR
DEGs
DESeq2
updated 17 hours ago by
swbarnes2
14k • written 19 hours ago by
BioinfGuru
★ 1.7k
1
vote
1
reply
197
views
Inconsistency in SNP detection pipelines for multi-sample analysis
vcf
bam
bcf
snps
updated 18 hours ago by
LChart
3.9k • written 20 hours ago by
George
▴ 10
0
votes
0
replies
100
views
Problem with Mirdeep2 and Randfold output
mirdeep2
Randfold
updated 18 hours ago by
Ram
43k • written 18 hours ago by
otieno43
▴ 20
0
votes
2
replies
243
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
4 hours ago by
Kai Xin
• 0
1
vote
1
reply
162
views
Retrieve a % coverage for each transcript
RNA-seq
updated 19 hours ago by
Ram
43k • written 20 hours ago by
jammydodger123456
▴ 40
0
votes
1
reply
279
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics
bootstrap
updated 20 hours ago by
Klaus S
▴ 150 • written 6 days ago by
Zeng Hao
▴ 40
0
votes
2
replies
252
views
How can I solve this error?
metal
9 hours ago by
22211020193
• 0
0
votes
0
replies
98
views
Struggling to lift genome builds
PLINK
liftover
GWAS
updated 20 hours ago by
GenoMax
141k • written 21 hours ago by
srimmer
• 0
1
vote
2
replies
195
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 19 hours ago by
Ram
43k • written 21 hours ago by
aniigodwinn
• 0
2
votes
3
replies
213
views
Sheep reference genome remapping coordinates
reference
remap
sheep
coordinates
genome
22 minutes ago by
valentinatsar
• 0
1
vote
3
replies
206
views
Editing Human Reference Genome by adding a CDS
gff
agat
transcriptome
updated 21 hours ago by
Michael
54k • written 22 hours ago by
LDT
▴ 330
0
votes
8
replies
382
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 19 hours ago by
Pierre Lindenbaum
161k • written 23 hours ago by
me
• 0
2
votes
1
reply
217
views
differential gene expression analysis when not all samples have an untreated counterpart
differential-expression
edgeR
updated 23 hours ago by
Gordon Smyth
★ 7.0k • written 8 days ago by
nhaus
▴ 300
0
votes
0
replies
178
views
Looking for an explanation as to what the Peak Score is from HOMER, not finding any answers on Biostars yet
Homer
ATAC-seq
23 hours ago by
Ronin
• 0
4
votes
2
replies
1.7k
views
How to convert SAM/BAM file to GTF/GFF file?
GTF
SAM
BAM
GFF
minimap2
updated 1 day ago by
Dr.Animo
▴ 130 • written 11 months ago by
BioinfoBee
• 0
2
votes
6
replies
521
views
Removing duplicates
duplicates
ONT
minimap2
4 hours ago by
quentinperriere
• 0
0
votes
1
reply
143
views
Annotating a dataset with gnomAD v4 using Hail
Python
Sequencing
Hail
Exome
Annotation
updated 1 day ago by
DKA
▴ 40 • written 1 day ago by
james.melhorn
• 0
3
votes
4
replies
240
views
biomaRt error for different R version
biomaRt
R
updated 57 minutes ago by
GenoMax
141k • written 1 day ago by
manaswwm
▴ 490
0
votes
1
reply
132
views
Freyja plot error
Freyja
updated 21 hours ago by
Ram
43k • written 1 day ago by
Adyasha
• 0
1
vote
2
replies
147
views
Interpretation of combined P values - RNA microarray meta analysis
metaanalysis
R
microarray
DExMA
combinedP
1 day ago by
hagl
▴ 10
0
votes
0
replies
96
views
BIOM format can contain tabular data ?
BIOM
phyloseq
biomformat
R
1 day ago by
chemokine-1
▴ 10
0
votes
4
replies
359
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
6 hours ago by
feather-W
• 0
0
votes
1
reply
159
views
Job:
Consultant to update a Snakemake workflow with the new Kubernetes executor plugin for Snakemake 8
Kubernetes
DevOps
executor
AWS
Snakemake
updated 1 day ago by
Michael
54k • written 1 day ago by
jonrkarr
▴ 100
0
votes
2
replies
164
views
Bedmethyl file format
bedmethyl
methylation
updated 1 day ago by
GenoMax
141k • written 1 day ago by
njornet
▴ 20
0
votes
0
replies
118
views
sequence table for DADA2 chimera filtering
OTU
sequencetable
DADA2
1 day ago by
Ali
• 0
2
votes
4
replies
252
views
SnpEff annotates coding duplication as intronic?
snpeff
1 day ago by
kirill.zaslavsky
• 0
0
votes
2
replies
190
views
Calculating percentage of cells proliferating in single cell rna seq data
statistics
scRNA-seq
proliferation
1 day ago by
mropri
▴ 150
0
votes
1
reply
216
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
updated 20 hours ago by
bk11
★ 2.3k • written 1 day ago by
航太郎
• 0
5
votes
4
replies
2.8k
views
genefu for PAM50 prediction
RNA-Seq
breast cancer
subtyping
updated 1 day ago by
hamarillo
▴ 70 • written 5.6 years ago by
silviajserrano
▴ 50
1,000 results • Page
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Recent Votes
Answer: differential gene expression analysis when not all samples have an untreated cou
Answer: differential gene expression analysis when not all samples have an untreated cou
Answer: Sheep reference genome remapping coordinates
Answer: Sheep reference genome remapping coordinates
DEG analysis of RNA-seq data across multiple tissues and two conditions
Answer: Assume "yes" as the answer to any prompts with bioconda
Answer: Assume "yes" as the answer to any prompts with bioconda
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Recent Replies
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
by
Elisabeth Gasteiger
★ 2.3k
See also https://www.uniprot.org/help/negative_datasets
Comment: Sheep reference genome remapping coordinates
by
valentinatsar
• 0
Thank you for your response As I can understand this tool takes sequence input files right? I have genome-wide genotypes instead of sequen…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
by
me
▴ 750
Ok I made this into an answer. Could you please accept it as such.
Answer: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
by
me
▴ 750
You can't. The data does not exist. UniProt only annotates where a lysine is know to be acetylated. There is no way that UniProt can know w…
Comment: How to compare the quality of assemblies
by
GenoMax
141k
Are there any short read datasets available in SRA? Can you try and see how many left over reads remain after you align to both of your ass…
Comment: Korean human genome reference file
by
GenoMax
141k
From NCBI: https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_001712695.1/ Use the `Download` button or `curl/datasets`.
Comment: SLURM submission problem: Indexing the Reference Genome is not done in STAR
by
GenoMax
141k
> But it keeps giving error Please tell us what the error is.
Answer: 10x VDJ (TCR/BCR) BAM to fastq
by
GenoMax
141k
Looking at the information about the BAM file in the link included at the end of this sentence, it seems that the BAM file does not contain…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
by
Jacky
• 0
I got it, thank you for your response.
Answer: DEseq2
by
ATpoint
81k
The DESeq2 input is a numeric count matrix (or data.frame) with rows being genes/observations and columns being samples/cells/specimen. Ple…
Comment: How to add motifs in cellranger-arc reference?
by
Ehsan
• 0
Hi. Do you have any updates on what you ended up doing? I am encountering same issue, cannot really find a good TF motif database for zebra…
Comment: biomaRt error for different R version
by
manaswwm
▴ 490
Wonderful, and thanks for tagging Mike! For those who come back for this problem, the following seemed to work for me: Downgrading `dbply…
Answer: Assume "yes" as the answer to any prompts with bioconda
by
Juke34
8.5k
From my experience using `biocontainers` base container no need to set `yes` installation is done without any command prompt, otherwise as …
Comment: SLURM submission problem: Indexing the Reference Genome is not done in STAR
by
Dave Carlson
★ 1.7k
You're allocating 4 compute nodes (`#SBATCH -N 4`), but STAR can't actually make use of more than 1 compute node. You can increase the num…
Answer: Assume "yes" as the answer to any prompts with bioconda
by
Dave Carlson
★ 1.7k
```conda install -y bioconda::packageX conda-forge::packageY``` should do what you're looking for.
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