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121,465 results • Page
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9
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twist exome panel analysis
twist
exome
17 minutes ago by
1769mkc
★ 1.3k
0
votes
0
replies
7
views
News:
In-Person NGS Epigenomics Workshop (November 3-5 in Munich, Germany)
ChIPSeq
BisulfiteSeq
ATACSeq
workshop
1 hour ago by
ecSeq Bioinformatics
▴ 20
0
votes
0
replies
16
views
News:
Announcing a New Journal – Bioinformatics Methods and Applications – Now Open for Submissions
bioinformatics
1 hour ago by
Wei
• 0
2
votes
1
reply
85
views
How to address conflicting circRNA expression results between public datasets and published studies? is it normal?
CicRNA-GEO
updated 54 minutes ago by
rfran010
★ 1.6k • written 11 hours ago by
ParastooA
▴ 20
0
votes
0
replies
58
views
Trouble removing adapters from sequences using cutadapt
removal
cutadapt
adapter
primer
11 hours ago by
k.lagan
• 0
1
vote
4
replies
133
views
Help for Pooled Exome Sequencing SNP Analysis
GATK
SNP
Exome
polymorphisms
10 hours ago by
alejandro.mejiam1
▴ 20
840
votes
170
replies
181k
views
112 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 8 weeks ago by
Biostar
3.6k • written 8.6 years ago by
Istvan Albert
102k
0
votes
0
replies
56
views
low variant sites similarity between linear reference and vg call path
call
vg
updated 16 hours ago by
GenoMax
152k • written 16 hours ago by
PolenP
• 0
0
votes
0
replies
70
views
KEGG pathways. How to plot the log2FC of genes collapsed into a "node"?
visualization
DEG
KEGG
R
pathway
17 hours ago by
txema.heredia
▴ 240
0
votes
1
reply
91
views
MACS3 Parameter adjustments
human
libraries
illumina
callpeak
macs3
updated 11 hours ago by
rfran010
★ 1.6k • written 17 hours ago by
María José
▴ 10
4
votes
1
reply
297
views
DeSeq2 how to change design matrix when samples are exclusive: error in “Model matrix not full rank” checkFullRank(full)
Deseq2
updated 1 hour ago by
ATpoint
88k • written 1 day ago by
totoroGirl
• 0
0
votes
1
reply
106
views
Interactive UMAP scanpy
UMAP
scanpy
interactive
updated 21 hours ago by
antonioggsousa
3.4k • written 22 hours ago by
npont
▴ 10
7
votes
5
replies
202
views
Can I use removeBatchEffect() before performing DEG analysis in bulk RNA-seq with limma-voom?
Batchcorrection
VOOM
DEGanalysis
Limma
bulkRNA
updated 16 hours ago by
i.sudbery
21k • written 23 hours ago by
Sumeet
▴ 10
5
votes
6
replies
382
views
Log2FC track Visualization in IGV
visualization
IGV
RNASeq
2 days ago by
SomeOne
▴ 220
0
votes
0
replies
61
views
News:
online course: Sex Chromosome Evolution - 6–10 October 2025
SexChromosome
Evolution
Genomics
1 day ago by
Physalia-courses
★ 2.6k
0
votes
0
replies
71
views
GSEA of sugarcane
GSEA
1 day ago by
analyst
▴ 70
3
votes
5
replies
445
views
DESeq2 design for differential expression with 2 timepoints and 2 controls
Transcriptomic
Feeding
DESeq2
RNAseq
updated 15 hours ago by
SamGG
▴ 150 • written 5 days ago by
Cristina
• 0
1
vote
12
replies
412
views
FeatureCount : Successfully assigned alignments is low
rnaseq
featurecount
23 hours ago by
HarperReed
• 0
1
vote
2
replies
172
views
Difficulties in calling peaks for CUT&RUN (IgG control with high RPKM value)
CUTRUN
calling
IgG
peak
22 hours ago by
Basti
★ 2.1k
7
votes
3
replies
302
views
custom BED to UCSC genome browser
browser
ucsc
ucsc-genome-browser
genome
methylation
bed
1 day ago by
npont
▴ 10
1
vote
2
replies
166
views
unmatched number of reads after trimming treatment by afterqc
NGS
genome
assembly
1 day ago by
德水
• 0
0
votes
1
reply
147
views
Extract Specific RNA-seq reads from BAM using deeptools
RNA-seq
deeptools
updated 1 day ago by
GenoMax
152k • written 2 days ago by
Qilin
• 0
0
votes
0
replies
107
views
check vsiRNA expression of mosquito (smallRNA seq data)
seq
expression
data
smallRNA
mosquito
vsiRNA
2 days ago by
ZuelTech
• 0
0
votes
11
replies
392
views
Error Correction with Tadpole and BBMerge
BBmerge
tadpole
error
correction
2 days ago by
Jon
• 0
2
votes
1
reply
145
views
Quantification for small RNAseq data
quantification
seq
data
smallRNA
updated 2 days ago by
rfran010
★ 1.6k • written 2 days ago by
ZuelTech
• 0
6
votes
4
replies
244
views
GrCh37 or GrCh38? That is the question.
GrCh37
sequence
human
genome
GrCh38
7 hours ago by
Anjan
▴ 840
0
votes
2
replies
396
views
Scvi - Integration
integration
singlecell
scvi
22 hours ago by
t.foskolos
• 0
4
votes
3
replies
283
views
Bootstrapping in RNA-seq
bootstrapping
RNAseq
updated 2 days ago by
rfran010
★ 1.6k • written 2 days ago by
littlebioinformatician
• 0
1
vote
2
replies
268
views
Computing ka/ks ratio for individual genes.
ks
ka
evolution
selection
16 hours ago by
Shakunthala Natarajan
• 0
1
vote
0
replies
308
views
Job:
Several Permanent Positions as Bioinformatician/Computational Biologist/System Developer/Project Leader at Swedish national research infrastructures
Sweden
SciLifeLab
Genomics
Uppsala
Proteomics
21 hours ago by
Matthias Zepper
5.1k
2
votes
2
replies
195
views
Obtaining a BED/GTF from Ensembl
rna-seq
ensembl
bcftools
rna
2 days ago by
joe_genome
▴ 60
0
votes
0
replies
141
views
News:
New Bioconductor and Physalia Collaboration!
Bioconductor
DataAnalysis
Genomics
2 days ago by
Physalia-courses
★ 2.6k
1
vote
1
reply
237
views
Read1 and read2 asymmetry in stranded, paired-end rnaseq data aligned by STAR
stranded
STAR
RNAseq
antisense
sense
updated 3 days ago by
rfran010
★ 1.6k • written 4 days ago by
yampolsk
▴ 10
0
votes
1
reply
228
views
Does the order of SplitNCigarReads and MarkDuplicates affect RNA-seq variant calling results?
variantcalling.
rnaseq
gatk
updated 3 days ago by
rfran010
★ 1.6k • written 4 days ago by
iamsmor
• 0
0
votes
0
replies
139
views
Should I standardize age and age2 as covariates in GWAS models?
GWAS
covariates
3 days ago by
yu
• 0
5
votes
6
replies
520
views
Venn Diagram
VennDiagram
updated 1 day ago by
lieven.sterck
15k • written 5 days ago by
Nasim Gandomdoust
• 0
0
votes
1
reply
188
views
PhageTerm error
phage
genome
phageterm
assamble
updated 2 days ago by
GenoMax
152k • written 3 days ago by
NIkita
• 0
0
votes
1
reply
180
views
WGCNA Workflow from GEO FASTQ Files – Expression Type, Sample Inclusion, and Preprocessing
fastq
wgcna
rna
updated 3 days ago by
GenoMax
152k • written 3 days ago by
tutorwhizzz
• 0
0
votes
0
replies
147
views
small RNA-Seq pipeline Standstill
NGS
miRNA
3 days ago by
anthony.santana.703.j
▴ 30
2
votes
3
replies
282
views
comparison interpretation
model
design
contrast
matrix
1 day ago by
jkim
▴ 200
0
votes
0
replies
151
views
piRNAs Analysis Pipelines
piRNAs
smallRNA
3 days ago by
GA
• 0
1
vote
1
reply
193
views
Beagle PATH (partially) recognised on Ubuntu 22.04
Ubuntu
Beagle
Beast
MCMC
updated 3 days ago by
GenoMax
152k • written 3 days ago by
Luca Arbore
▴ 10
0
votes
0
replies
171
views
CNV Computation with HoneyBadger
CNV
HoneyBADGER
updated 3 days ago by
GenoMax
152k • written 3 days ago by
mete.han.celebi
• 0
0
votes
0
replies
167
views
How to predict programatically TFBS and calculate PWM Score as JASPAR
PWMScan
TFBS
JASPAR
4 days ago by
t.kajiyama
• 0
0
votes
0
replies
390
views
News:
Hands-On Workshop - Next-Generation Sequencing Data Analysis: A Practical Introduction (September 10-12, 2025 in Berlin, Germany)
Workshop
RNA-Seq
Illumina
VariantCalling
DNA-Seq
4 days ago by
ecSeq Bioinformatics
▴ 20
0
votes
14
replies
704
views
Host Removal Issues Human/Dog with samples containing Eukaryotic species
Eukarotic
Mapping
Host
updated 4 days ago by
Mensur Dlakic
★ 29k • written 5 days ago by
Jon
• 0
1
vote
1
reply
274
views
Pharokka Error
error
annotating
viral
pharokka
genome
updated 4 days ago by
Mensur Dlakic
★ 29k • written 4 days ago by
NIkita
• 0
0
votes
0
replies
191
views
Combining Metatranscriptomics (Mtx) and Metagenomics (Mgx)
metagenomics
reference-based
Metatranscriptomics
alignment
updated 4 days ago by
GenoMax
152k • written 4 days ago by
rk009
• 0
1
vote
1
reply
262
views
how to make a circular plot of variants
circular
plot
updated 4 days ago by
Pierre Lindenbaum
166k • written 4 days ago by
analyst
▴ 70
2
votes
6
replies
441
views
GSEA analysis
RNA-seq
RNA
analysis
updated 4 days ago by
GenoMax
152k • written 5 days ago by
Ahmed
• 0
121,465 results • Page
1 of 2430
Recent Votes
Comment: Can I use removeBatchEffect() before performing DEG analysis in bulk RNA-seq wit
Answer: GrCh37 or GrCh38? That is the question.
Answer: GrCh37 or GrCh38? That is the question.
Answer: GrCh37 or GrCh38? That is the question.
DESeq2 contrasts - creating different objects or not?
C: DESeq2 contrasts - creating different objects or not?
Comment: Help for Pooled Exome Sequencing SNP Analysis
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Comment: How to address conflicting circRNA expression results between public datasets an
by
rfran010
★ 1.6k
> 1. How should I acknowledge and discuss this discrepancy in a paper or thesis? The differences you mention is a good start. Would need …
Comment: GrCh37 or GrCh38? That is the question.
by
Anjan
▴ 840
Thank you @genomax. Heng Li's blog was helpful.
Comment: Help for Pooled Exome Sequencing SNP Analysis
by
alejandro.mejiam1
▴ 20
You mean joining and then obtaining the SNPs that are only present in my resistant treatment?
Comment: Help for Pooled Exome Sequencing SNP Analysis
by
alejandro.mejiam1
▴ 20
Hi! - nohup is for avoiding internet disconnections on the server I work as is my understanding - What do you mean by the 2 option? th…
Comment: MACS3 Parameter adjustments
by
rfran010
★ 1.6k
What's type of data is this? e.g. chip-seq? That seems like a high duplication rate. Is this data enriched for telomere sequences? `-B` a…
Comment: Help for Pooled Exome Sequencing SNP Analysis
by
Pierre Lindenbaum
166k
1) using `nohup` is most always a bad idea . Learn screen/tmux, learn make/nextflow/snakemake 2) AddOrReplaceReadGroups should be useless…
Answer: Help for Pooled Exome Sequencing SNP Analysis
by
Pierre Lindenbaum
166k
call all your bams in one HaplotypeCaller call (= "joint calling vcf" ) use a tool to find the variants present in a subset of sample…
Comment: DESeq2 design for differential expression with 2 timepoints and 2 controls
by
SamGG
▴ 150
Having a similar design and a new column of colData that is time_condition, could you confirm that for 4, the model with interaction leads …
Comment: Can I use removeBatchEffect() before performing DEG analysis in bulk RNA-seq wit
by
i.sudbery
21k
You should explicitly model batch in each new DEG contrast.
Comment: Computing ka/ks ratio for individual genes.
by
Shakunthala Natarajan
• 0
Hi. Thank you. I will look into PAML.
Comment: Interactive UMAP scanpy
by
antonioggsousa
3.4k
I think you should be able to use `plotly` ([docs](https://plotly.com/python/)). The UMAP plot is just a scatter plot. I think it should be…
Comment: Can I use removeBatchEffect() before performing DEG analysis in bulk RNA-seq wit
by
Sumeet
▴ 10
Hi @atpoint and @iansudbery Thank you for the helpful explanation, I really appreciate the clarity. Following up: I used removeBatchEf…
Comment: Can I use removeBatchEffect() before performing DEG analysis in bulk RNA-seq wit
by
Sumeet
▴ 10
Hi Ian, Thank you for your response.
Answer: DeSeq2 how to change design matrix when samples are exclusive: error in “Model m
by
i.sudbery
21k
This is an example of what the edgeR manual refers to as a "with and between" design. See page 44 of the edgeR user's guide here: https://w…
Comment: Can I use removeBatchEffect() before performing DEG analysis in bulk RNA-seq wit
by
i.sudbery
21k
TLDR: You don't need to run removeBatchEffects, because voom will automatically remove the batch effects if you tell it about them.
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