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116,465 results • Page
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traying to make a maf from an already annotated vcf
vcf2maf
VEP
maftools
updated just now by
Ram
43k • written 2 minutes ago by
Javier
• 0
1
vote
4
replies
424
views
What happened to Tombo Re-squiggle
Tombo
resquiggle
ONT
updated 7 minutes ago by
Ram
43k • written 3 months ago by
turcoa1
• 0
0
votes
0
replies
12
views
Pruning with plink finds a majority of SNPs in very high LD
LD
SNP
plink
pruning
22 minutes ago by
enferdeflame
• 0
0
votes
0
replies
11
views
Difference when using difference number of pathways score to compare between 3 groups
Limma
GSVA
20 minutes ago by
Chris
▴ 260
0
votes
1
reply
29
views
change gene IDs to gene name in RNAseq
RNA-seq
GTF
R
updated 41 minutes ago by
Trivas
★ 1.7k • written 1 hour ago by
mrymrahimi70
• 0
0
votes
0
replies
38
views
News:
Online course: Meta-analysis in R
Meta-Analysis
Statistics
R
updated 43 minutes ago by
Ram
43k • written 2 hours ago by
carlopecoraro2
★ 2.5k
1
vote
9
replies
442
views
How can I retrieve wheat lysine non-acetylated sequences from the UniProt database?
UniProt
updated 2 hours ago by
Elisabeth Gasteiger
★ 2.4k • written 6 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
107
views
10x VDJ (TCR/BCR) BAM to fastq
TCR
VDJ
BCR
10x
updated 3 hours ago by
GenoMax
141k • written 4 hours ago by
predeus
★ 1.9k
0
votes
1
reply
122
views
DEseq2
RNA-seq
DESeq2
updated 43 minutes ago by
Ram
43k • written 5 hours ago by
rrehimi
• 0
0
votes
0
replies
46
views
News:
Course - Agent-Based Modelling Using NetLogo - University of Lodz, Poland
Netlogo
Individual-Based-Models
Agent-Based-Models
updated 42 minutes ago by
Ram
43k • written 4 hours ago by
carlopecoraro2
★ 2.5k
4
votes
2
replies
184
views
Assume "yes" as the answer to any prompts with bioconda
docker
container
bioconda
updated 4 hours ago by
Juke34
8.5k • written 4 hours ago by
njornet
▴ 20
0
votes
0
replies
52
views
Tutorial:
DNA Methylation: Sequencing Techniques
WGBS
RRBS
4 hours ago by
Novogene
▴ 410
0
votes
1
reply
343
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree
microbiome
updated 40 minutes ago by
Ram
43k • written 19 months ago by
Muhammad
• 0
1
vote
2
replies
173
views
Korean human genome reference file
GWAS
reference
imputation
updated 2 hours ago by
GenoMax
141k • written 6 hours ago by
SeoGyun
• 0
1
vote
4
replies
272
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
updated 2 hours ago by
GenoMax
141k • written 6 hours ago by
n_navy
• 0
0
votes
2
replies
173
views
RNA seq differential expression analysis
RNA-seq
normalization
updated 46 minutes ago by
Ram
43k • written 6 hours ago by
rrehimi
• 0
0
votes
1
reply
118
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
updated 2 hours ago by
GenoMax
141k • written 6 hours ago by
kirillkirilenko
▴ 20
0
votes
0
replies
53
views
How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau-score
tspex
updated 35 minutes ago by
Ram
43k • written 7 hours ago by
bioinfo223
▴ 10
0
votes
0
replies
65
views
How to root an unrooted tree with a known root tree?
phylogenetics
rooting
R
7 hours ago by
P.
• 0
0
votes
0
replies
69
views
Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
snpEff
9 hours ago by
ekirsch
• 0
0
votes
0
replies
99
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
14 hours ago by
renan.igor
• 0
1
vote
1
reply
163
views
Pediococcus acidilactici sequence analysis
BLAST
Gene-Ontology
updated 10 hours ago by
Ram
43k • written 16 hours ago by
anasjamshed
▴ 120
3
votes
1
reply
533
views
What is the normalization status of metabric data?
metabric
normalization
microarray
cbioportal
updated 15 hours ago by
etiennedanis
▴ 20 • written 19 months ago by
DareDevil
★ 4.3k
0
votes
0
replies
89
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
16 hours ago by
synat.keam
▴ 100
0
votes
1
reply
177
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 18 hours ago by
GenoMax
141k • written 18 hours ago by
ycts
• 0
2
votes
3
replies
373
views
DEG analysis of RNA-seq data across multiple tissues and two conditions
RNA-seq
EdgeR
DEGs
DESeq2
updated 19 hours ago by
swbarnes2
14k • written 21 hours ago by
BioinfGuru
★ 1.7k
1
vote
1
reply
206
views
Inconsistency in SNP detection pipelines for multi-sample analysis
vcf
bam
bcf
snps
updated 20 hours ago by
LChart
3.9k • written 22 hours ago by
George
▴ 10
0
votes
0
replies
107
views
Problem with Mirdeep2 and Randfold output
mirdeep2
Randfold
updated 20 hours ago by
Ram
43k • written 20 hours ago by
otieno43
▴ 20
0
votes
2
replies
253
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
6 hours ago by
Kai Xin
• 0
1
vote
1
reply
168
views
Retrieve a % coverage for each transcript
RNA-seq
updated 22 hours ago by
Ram
43k • written 22 hours ago by
jammydodger123456
▴ 40
0
votes
1
reply
285
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics
bootstrap
updated 22 hours ago by
Klaus S
▴ 150 • written 6 days ago by
Zeng Hao
▴ 40
0
votes
2
replies
260
views
How can I solve this error?
metal
11 hours ago by
22211020193
• 0
0
votes
0
replies
102
views
Struggling to lift genome builds
PLINK
liftover
GWAS
updated 22 hours ago by
GenoMax
141k • written 23 hours ago by
srimmer
• 0
1
vote
2
replies
199
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 21 hours ago by
Ram
43k • written 23 hours ago by
aniigodwinn
• 0
2
votes
3
replies
257
views
Sheep reference genome remapping coordinates
reference
remap
sheep
coordinates
genome
2 hours ago by
valentinatsar
• 0
1
vote
3
replies
211
views
Editing Human Reference Genome by adding a CDS
gff
agat
transcriptome
updated 23 hours ago by
Michael
54k • written 1 day ago by
LDT
▴ 330
0
votes
9
replies
394
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated just now by
jkbonfield
★ 1.2k • written 1 day ago by
me
• 0
2
votes
1
reply
224
views
differential gene expression analysis when not all samples have an untreated counterpart
differential-expression
edgeR
updated 1 day ago by
Gordon Smyth
★ 7.0k • written 8 days ago by
nhaus
▴ 300
0
votes
0
replies
188
views
Looking for an explanation as to what the Peak Score is from HOMER, not finding any answers on Biostars yet
Homer
ATAC-seq
1 day 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
532
views
Removing duplicates
duplicates
ONT
minimap2
7 hours ago by
quentinperriere
• 0
0
votes
1
reply
146
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
286
views
biomaRt error for different R version
biomaRt
R
updated 3 hours ago by
GenoMax
141k • written 1 day ago by
manaswwm
▴ 490
0
votes
1
reply
135
views
Freyja plot error
Freyja
updated 23 hours ago by
Ram
43k • written 1 day ago by
Adyasha
• 0
1
vote
2
replies
151
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
100
views
BIOM format can contain tabular data ?
BIOM
phyloseq
biomformat
R
1 day ago by
chemokine-1
▴ 10
0
votes
4
replies
367
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
8 hours ago by
feather-W
• 0
0
votes
1
reply
164
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
168
views
Bedmethyl file format
bedmethyl
methylation
updated 1 day ago by
GenoMax
141k • written 1 day ago by
njornet
▴ 20
116,465 results • Page
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Comment: Trying to write bwa mem -> samtools view -> samtools sort loop
C: Extract fasta sequences from a file using a list in another file.
A: Extract fasta sequences from a file using a list in another file.
How to comparing two bacterial genomes and find the mutation, rearrangement etc.
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
Answer: Korean reference file
How to get all genes for a specific list of regions in R preferably using Biomart
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Comment: Questions about a bug when transferring cram file to bam file
by
jkbonfield
★ 1.2k
That SQ M5 is chr1 in my copy of GRCh38 (Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa). I'm assuming your hg38.fa is not the sa…
Comment: What happened to Tombo Re-squiggle
by
Ram
43k
Please do not add answers unless you're answering the top level question. Instead, use `Add Comment` or `Add Reply` as appropriate. I've mo…
Comment: What happened to Tombo Re-squiggle
by
Joseph
• 0
Hi, Does anybody has the answer to this? I also want to resquiggle my data with Remora but do not quite get which is the appropriate com…
Answer: change gene IDs to gene name in RNAseq
by
Trivas
★ 1.7k
This has been answered a million times on this forum, see here https://www.biostars.org/p/430015/
Comment: How To Identify The 16S Rrna Gene Sequence In A Genome
by
colindaven
6.3k
It's also worth mentioning `Barrnap` is in the bacterial annotation system **Prokka**. `Prokka` can be installed on Debian systems with `…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
by
Elisabeth Gasteiger
★ 2.4k
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…
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