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121,467 results • Page
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29
views
DGE analysis in Seurat using paired samples per donor ?
paired
seurat
dge
sample
2 hours ago by
Picasa
▴ 680
1
vote
2
replies
104
views
Deseq2
PyDeseq2
Deseq2
updated 1 hour ago by
GenoMax
152k • written 9 hours ago by
sk_24
▴ 10
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
1
vote
1
reply
98
views
twist exome panel analysis
twist
exome
updated 9 hours ago by
GenoMax
152k • written 14 hours ago by
1769mkc
★ 1.3k
0
votes
0
replies
55
views
News:
In-Person NGS Epigenomics Workshop (November 3-5 in Munich, Germany)
ChIPSeq
BisulfiteSeq
ATACSeq
workshop
15 hours ago by
ecSeq Bioinformatics
▴ 20
0
votes
0
replies
67
views
News:
Announcing a New Journal – Bioinformatics Methods and Applications – Now Open for Submissions
bioinformatics
15 hours ago by
Wei
• 0
2
votes
1
reply
168
views
How to address conflicting circRNA expression results between public datasets and published studies? is it normal?
CicRNA-GEO
updated 15 hours ago by
rfran010
★ 1.6k • written 1 day ago by
ParastooA
▴ 20
0
votes
4
replies
174
views
Trouble removing adapters from sequences using cutadapt
removal
cutadapt
adapter
primer
updated 3 hours ago by
GenoMax
152k • written 1 day ago by
k.lagan
• 0
1
vote
6
replies
224
views
Help for Pooled Exome Sequencing SNP Analysis
GATK
SNP
Exome
polymorphisms
6 hours ago by
alejandro.mejiam1
▴ 20
0
votes
0
replies
80
views
low variant sites similarity between linear reference and vg call path
call
vg
updated 1 day ago by
GenoMax
152k • written 1 day ago by
PolenP
• 0
0
votes
0
replies
90
views
KEGG pathways. How to plot the log2FC of genes collapsed into a "node"?
visualization
DEG
KEGG
R
pathway
1 day ago by
txema.heredia
▴ 240
0
votes
3
replies
164
views
MACS3 Parameter adjustments
human
libraries
illumina
callpeak
macs3
updated 9 hours ago by
ATpoint
88k • written 1 day ago by
María José
▴ 10
4
votes
1
reply
348
views
DeSeq2 how to change design matrix when samples are exclusive: error in “Model matrix not full rank” checkFullRank(full)
Deseq2
updated 15 hours ago by
ATpoint
88k • written 2 days ago by
totoroGirl
• 0
0
votes
1
reply
141
views
Interactive UMAP scanpy
UMAP
scanpy
interactive
updated 1 day ago by
antonioggsousa
3.4k • written 1 day ago by
npont
▴ 10
9
votes
5
replies
243
views
Can I use removeBatchEffect() before performing DEG analysis in bulk RNA-seq with limma-voom?
Batchcorrection
VOOM
DEGanalysis
Limma
bulkRNA
updated 1 day ago by
i.sudbery
21k • written 1 day ago by
Sumeet
▴ 10
7
votes
5
replies
419
views
Log2FC track Visualization in IGV
visualization
IGV
RNASeq
3 days ago by
SomeOne
▴ 240
0
votes
0
replies
79
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
87
views
GSEA of sugarcane
GSEA
1 day ago by
analyst
▴ 70
4
votes
6
replies
503
views
DESeq2 design for differential expression with 2 timepoints and 2 controls
Transcriptomic
Feeding
DESeq2
RNAseq
updated 10 hours ago by
txema.heredia
▴ 240 • written 6 days ago by
Cristina
• 0
1
vote
12
replies
442
views
FeatureCount : Successfully assigned alignments is low
rnaseq
featurecount
1 day ago by
HarperReed
• 0
1
vote
2
replies
195
views
Difficulties in calling peaks for CUT&RUN (IgG control with high RPKM value)
CUTRUN
calling
IgG
peak
1 day ago by
Basti
★ 2.1k
7
votes
3
replies
326
views
custom BED to UCSC genome browser
browser
ucsc
ucsc-genome-browser
genome
methylation
bed
2 days ago by
npont
▴ 10
1
vote
2
replies
183
views
unmatched number of reads after trimming treatment by afterqc
NGS
genome
assembly
2 days ago by
德水
• 0
0
votes
1
reply
165
views
Extract Specific RNA-seq reads from BAM using deeptools
RNA-seq
deeptools
updated 2 days ago by
GenoMax
152k • written 2 days ago by
Qilin
• 0
0
votes
0
replies
127
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
423
views
Error Correction with Tadpole and BBMerge
BBmerge
tadpole
error
correction
2 days ago by
Jon
• 0
2
votes
1
reply
159
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
277
views
GrCh37 or GrCh38? That is the question.
GrCh37
sequence
human
genome
GrCh38
21 hours ago by
Anjan
▴ 840
0
votes
2
replies
415
views
Scvi - Integration
integration
singlecell
scvi
1 day ago by
t.foskolos
• 0
4
votes
3
replies
303
views
Bootstrapping in RNA-seq
bootstrapping
RNAseq
updated 2 days ago by
rfran010
★ 1.6k • written 3 days ago by
littlebioinformatician
• 0
1
vote
2
replies
290
views
Computing ka/ks ratio for individual genes.
ks
ka
evolution
selection
1 day ago by
Shakunthala Natarajan
• 0
1
vote
0
replies
362
views
Job:
Several Permanent Positions as Bioinformatician/Computational Biologist/System Developer/Project Leader at Swedish national research infrastructures
Sweden
SciLifeLab
Genomics
Uppsala
Proteomics
1 day ago by
Matthias Zepper
5.1k
2
votes
2
replies
215
views
Obtaining a BED/GTF from Ensembl
rna-seq
ensembl
bcftools
rna
3 days ago by
joe_genome
▴ 60
0
votes
0
replies
157
views
News:
New Bioconductor and Physalia Collaboration!
Bioconductor
DataAnalysis
Genomics
3 days ago by
Physalia-courses
★ 2.6k
1
vote
1
reply
258
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
246
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 5 days ago by
iamsmor
• 0
0
votes
0
replies
161
views
Should I standardize age and age2 as covariates in GWAS models?
GWAS
covariates
3 days ago by
yu
• 0
5
votes
6
replies
538
views
Venn Diagram
VennDiagram
updated 2 days ago by
lieven.sterck
15k • written 6 days ago by
Nasim Gandomdoust
• 0
0
votes
1
reply
213
views
PhageTerm error
phage
genome
phageterm
assamble
updated 3 days ago by
GenoMax
152k • written 3 days ago by
NIkita
• 0
0
votes
1
reply
197
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
163
views
small RNA-Seq pipeline Standstill
NGS
miRNA
3 days ago by
anthony.santana.703.j
▴ 30
2
votes
3
replies
303
views
comparison interpretation
model
design
contrast
matrix
2 days ago by
jkim
▴ 200
0
votes
0
replies
171
views
piRNAs Analysis Pipelines
piRNAs
smallRNA
4 days ago by
GA
• 0
1
vote
1
reply
213
views
Beagle PATH (partially) recognised on Ubuntu 22.04
Ubuntu
Beagle
Beast
MCMC
updated 4 days ago by
GenoMax
152k • written 4 days ago by
Luca Arbore
▴ 10
0
votes
0
replies
187
views
CNV Computation with HoneyBadger
CNV
HoneyBADGER
updated 4 days ago by
GenoMax
152k • written 4 days ago by
mete.han.celebi
• 0
0
votes
0
replies
182
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
405
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
736
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
296
views
Pharokka Error
error
annotating
viral
pharokka
genome
updated 5 days ago by
Mensur Dlakic
★ 29k • written 5 days ago by
NIkita
• 0
0
votes
0
replies
208
views
Combining Metatranscriptomics (Mtx) and Metagenomics (Mgx)
metagenomics
reference-based
Metatranscriptomics
alignment
updated 5 days ago by
GenoMax
152k • written 5 days ago by
rk009
• 0
121,467 results • Page
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labelling the clusters from the CD4 T cell scRNAseq data
Answer: twist exome panel analysis
Deseq2
Gene set enrichment analysis with logFC and PValue
Comment: Removing duplicates
how to know what adapter sequences to trim for RNA-seq?
Answer: DESeq2 design for differential expression with 2 timepoints and 2 controls
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Comment: Deseq2
by
sk_24
• 0
@atpoint I am using PyDeseq2 package and tried running it for 4 conditions; A,B,C and D (each condition is a sample treated with different…
Comment: Trouble removing adapters from sequences using cutadapt
by
GenoMax
152k
> I am still seeing overrepresented sequences Isn't that expected since you are working with 16S (since the sequences are identical they …
Comment: Trouble removing adapters from sequences using cutadapt
by
k.lagan
• 0
**Update:** I found the adapter list from FastQC (https://github.com/golharam/FastQC/blob/master/Configuration/adapter_list.txt) and used t…
Comment: Help for Pooled Exome Sequencing SNP Analysis
by
alejandro.mejiam1
▴ 20
I understand now. Any experience on the pooled exome seq?
Comment: Trouble removing adapters from sequences using cutadapt
by
k.lagan
• 0
A little bit of both. I used the cutadapt website (https://cutadapt.readthedocs.io/en/stable/recipes.html) to learn the syntax and paramete…
Comment: MACS3 Parameter adjustments
by
ATpoint
88k
If these have MAPQ of 0 then you are probably forced to convert to BEDPE format and go along with this file as (I guess) macs will ignore r…
Answer: Deseq2
by
ATpoint
88k
The minimum is two conditions and at least one group with 2 replicates. Everything beyond that is basically possible, given you're not tryi…
Answer: twist exome panel analysis
by
GenoMax
152k
> do i need to run deduplication step before going into downstream? Yes. Based on their recommendation. https://www.twistbioscience.com/bl…
Comment: Trouble removing adapters from sequences using cutadapt
by
GenoMax
152k
> Below is the code I used to run cutadapt for my samples. Is that part of a pipeline or something you came up yourself? If former, can …
Comment: Help for Pooled Exome Sequencing SNP Analysis
by
GenoMax
152k
> nohup is for avoiding internet disconnections on the server I work as is my understanding Your server should have a program called `tmux…
Comment: Single-cell RNA Sequencing - transcript abundance estimation using Alevin-Fry
by
GenoMax
152k
There is a specific 5' kit: https://www.10xgenomics.com/products/universal-five-prime-gene-expression The difference between the 3' and 5'…
Comment: DESeq2 design for differential expression with 2 timepoints and 2 controls
by
txema.heredia
▴ 240
As far as I understand interaction designs, `timepoint6h.conditionFed` should show you if there is any synergistic effect between diet and …
Comment: MACS3 Parameter adjustments
by
María José
▴ 10
thanks @rfran010, I'm working with DNA that has been probe-selected using biotinylated telomeric repeats, which are then captured with stre…
Comment: Single-cell RNA Sequencing - transcript abundance estimation using Alevin-Fry
by
wooh
• 0
Apologies, one sequencing protocol describes loading the cell suspension into chips with 3 prime v3 chemistry and barcoded with 10 genomics…
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 …
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