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82 results • Page
2 of 2
Sort: replies
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0
votes
2
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158
views
Bedmethyl file format
bedmethyl
methylation
updated 21 hours ago by
GenoMax
141k • written 1 day ago by
njornet
▴ 20
0
votes
2
replies
199
views
VCF annotation with gnomADv4 using R package
annotation
gnomADv4
R
VCF
21 hours ago by
DKA
▴ 40
0
votes
2
replies
331
views
Which experiments generate Position Frequency Matrix?
Position-Frequency-Matrix
17 hours ago by
arriyaz.nstu
▴ 30
2
votes
1
reply
3.1k
views
Batch effect correction in DE analysis of single cell RNA-seq data and visualization
Seurat
Batch-effect
SCDE
RNA-Seq
Limma
updated 15 hours ago by
Ram
43k • written 5.5 years ago by
Poorya Parvizi
▴ 60
0
votes
1
reply
134
views
Annotating a dataset with gnomAD v4 using Hail
Python
Sequencing
Hail
Exome
Annotation
updated 21 hours ago by
DKA
▴ 40 • written 23 hours ago by
james.melhorn
• 0
0
votes
1
reply
206
views
differential gene expression analysis when not all samples have an untreated counterpart
differential-expression
edgeR
updated 20 hours ago by
Gordon Smyth
★ 7.0k • written 8 days ago by
nhaus
▴ 300
0
votes
1
reply
124
views
Freyja plot error
Freyja
updated 18 hours ago by
Ram
43k • written 23 hours ago by
Adyasha
• 0
0
votes
1
reply
272
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics
bootstrap
updated 16 hours ago by
Klaus S
▴ 150 • written 6 days ago by
Zeng Hao
▴ 40
1
vote
1
reply
151
views
Retrieve a % coverage for each transcript
RNA-seq
updated 16 hours ago by
Ram
43k • written 16 hours ago by
jammydodger123456
▴ 40
0
votes
1
reply
203
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
updated 16 hours ago by
bk11
★ 2.3k • written 1 day ago by
航太郎
• 0
0
votes
1
reply
1.2k
views
Controlling for batch effect in SNP-based PCA
whole-genome
PCA
batch-effect
SNP
updated 15 hours ago by
Ram
43k • written 4.7 years ago by
Ace
▴ 90
0
votes
1
reply
824
views
How to compare differentially expressed genes among different affymatrix dataset
microarray
batch-effect
R
updated 15 hours ago by
Ram
43k • written 4.8 years ago by
Calangoa
▴ 30
1
vote
1
reply
1.3k
views
Can we use previous estimated ComBat model to correct batch effects for new data?
microarray
RNA-Seq
batch-effect
updated 15 hours ago by
Ram
43k • written 5.0 years ago by
Min Dai
▴ 160
0
votes
1
reply
1.3k
views
About BatchQC packages error
Batch-effect
R
updated 15 hours ago by
Ram
43k • written 6.0 years ago by
Jun
• 0
1
vote
1
reply
188
views
Inconsistency in SNP detection pipelines for multi-sample analysis
vcf
bam
bcf
snps
updated 14 hours ago by
LChart
3.9k • written 16 hours ago by
George
▴ 10
0
votes
1
reply
2.7k
views
Can't make sva comparison despite very distinct batch effects
sva
batch-effect
updated 13 hours ago by
Ram
43k • written 6.2 years ago by
jjrin
▴ 40
0
votes
1
reply
156
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 12 hours ago by
GenoMax
141k • written 12 hours ago by
ycts
• 0
2
votes
1
reply
519
views
What is the normalization status of metabric data?
metabric
normalization
microarray
cbioportal
updated 9 hours ago by
etiennedanis
▴ 10 • written 19 months ago by
DareDevil
★ 4.3k
0
votes
1
reply
143
views
Pediococcus acidilactici sequence analysis
BLAST
Gene-Ontology
updated 4 hours ago by
Ram
43k • written 10 hours ago by
anasjamshed
▴ 120
0
votes
1
reply
32
views
Korean human genome reference file
GWAS
reference
imputation
updated 15 minutes ago by
colindaven
6.3k • written 59 minutes ago by
SeoGyun
• 0
0
votes
0
replies
75
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
8 hours ago by
renan.igor
• 0
0
votes
0
replies
32
views
How to root an unrooted tree with a known root tree?
phylogenetics
rooting
R
1 hour ago by
P.
• 0
0
votes
0
replies
19
views
How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau
score
tspex
1 hour ago by
bioinfo223
▴ 10
0
votes
0
replies
70
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
10 hours ago by
synat.keam
▴ 100
0
votes
0
replies
90
views
Problem with Mirdeep2 and Randfold output
mirdeep2
Randfold
updated 14 hours ago by
Ram
43k • written 15 hours ago by
otieno43
▴ 20
0
votes
0
replies
1.7k
views
Batch effect and CCA
CCA
RNA-Seq
seurat
batch-effect
updated 15 hours ago by
Ram
43k • written 5.1 years ago by
akivab2
▴ 110
0
votes
0
replies
1.1k
views
Should batch correction be performed before or after feature selection in scRNA-seq
batch-effect
scRNA-seq
feature-selection
updated 15 hours ago by
Ram
43k • written 4.9 years ago by
Lucy
▴ 140
0
votes
0
replies
89
views
Struggling to lift genome builds
PLINK
liftover
GWAS
updated 16 hours ago by
GenoMax
141k • written 17 hours ago by
srimmer
• 0
0
votes
0
replies
146
views
Looking for an explanation as to what the Peak Score is from HOMER, not finding any answers on Biostars yet
Homer
ATAC-seq
20 hours ago by
Ronin
• 0
0
votes
0
replies
6
views
DEseq2
RNA
DESeq2
seq
10 minutes ago by
rrehimi
• 0
0
votes
0
replies
25
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
updated 19 minutes ago by
colindaven
6.3k • written 1 hour ago by
kirillkirilenko
▴ 20
0
votes
0
replies
49
views
Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
snpEff
4 hours ago by
ekirsch
• 0
82 results • Page
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Comment: Removing duplicates
Comment: Removing duplicates
High fold change values
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Recent Replies
Comment: Indexing the Reference Genome is not done in STAR
by
n_navy
• 0
I add these parameters; #SBATCH -N 4 #SBATCH --tasks=1 #SBATCH -c 4 #SBATCH --time=24:00:00 But it keeps giving error
Comment: RNA seq differential expression analysis
by
rrehimi
• 0
Thanks! Could you please explain the DEseq2 method using Galaxy step by step? Input files?
Answer: Korean reference file
by
colindaven
6.3k
Is is this one - KOREF ? There might be multiple versions. https://www.ncbi.nlm.nih.gov/bioproject/PRJNA294231/ If it is, then take that…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
by
me
▴ 750
The question is not quite clear? are you asking for wheat proteins in UniProtKB which contain a lysine amino-acid, where those lysine are *…
Comment: RNA seq differential expression analysis
by
seta
★ 1.9k
You should provide row count (without normalization) for doing DEG analysis by relevant tools such as, edgeR or DEseq.
Comment: GSEA analysis in R
by
Sudip
• 0
Thank you. I have another question. Is there a way to get the gene list under "setSize" from the output that you gave as an example.
Comment: Per base sequence content failed miserably
by
Kai Xin
• 0
Hi, i have added the fastqc plots (untrimmed and trimmed). The sample was from anaerobes enriched from wastewater treatment plant, and this…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
by
Pierre Lindenbaum
161k
> lysine non-acetylated sequences what does it look like in uniprot ? give us an example with a uniprot identifier.
Answer: Indexing the Reference Genome is not done in STAR
by
Pierre Lindenbaum
161k
> CPU time limit exceeded your command is taking too long and can't be completed. check your cluster documentation to allocate more …
Comment: Removing duplicates
by
quentinperriere
• 0
thank you for responding. I was looking for suitable variant calling tool. I'm working on fungus and I don't have fast5 files. Could you re…
Comment: How to reduce the variation of CIBERSORTx results?
by
feather-W
• 0
Hi LChart, Thanks for your reply. I see S-mode in the CIBERSORTx official website tutorial(https://cibersortx.stanford.edu/), and the imag…
Comment: How to reduce the variation of CIBERSORTx results?
by
LChart
3.9k
First time I've heard of S-mode. I imagine you've seen this benchmark where it doesn't come out too well: https://academic.oup.com/bib/arti…
Comment: ISCN annotation for SV/CN VCF files
by
adedare
• 0
https://res.saletool.cn/vcf/18084521725806
Comment: ISCN annotation for SV/CN VCF files
by
adedare
• 0
https://res.saletool.cn/vcf/18084435127462
Comment: How can I solve this error?
by
22211020193
• 0
I want to conduct GWAS meta-analysis using metal software.
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