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121,452 results • Page
1 of 2430
Sort: Rank
Rank
Views
Votes
Replies
3
votes
4
replies
325
views
DESeq2 design for differential expression with 2 timepoints and 2 controls
Transcriptomic
Feeding
DESeq2
RNAseq
3 hours ago by
Cristina
• 0
1
vote
10
replies
283
views
FeatureCount : Successfully assigned alignments is low
rnaseq
featurecount
updated 8 hours ago by
CFierro
• 0 • written 17 hours ago by
HarperReed
• 0
0
votes
0
replies
119
views
DeSeq2 how to change design matrix when samples are exclusive: error in “Model matrix not full rank” checkFullRank(full)
Deseq2
7 hours ago by
totoroGirl
• 0
0
votes
1
reply
85
views
Difficulties in calling peaks for CUT&RUN (IgG control with high RPKM value)
CUTRUN
calling
IgG
peak
updated 11 hours ago by
ATpoint
88k • written 12 hours ago by
Basti
★ 2.1k
840
votes
170
replies
180k
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
7
votes
3
replies
244
views
custom BED to UCSC genome browser
browser
ucsc
ucsc-genome-browser
genome
methylation
bed
14 hours ago by
npont
▴ 10
1
vote
2
replies
104
views
unmatched number of reads after trimming treatment by afterqc
NGS
genome
assembly
5 hours ago by
德水
• 0
0
votes
1
reply
102
views
Extract Specific RNA-seq reads from BAM using deeptools
RNA-seq
deeptools
updated 14 hours ago by
GenoMax
152k • written 20 hours ago by
Qilin
• 0
0
votes
0
replies
67
views
check vsiRNA expression of mosquito (smallRNA seq data)
seq
expression
data
smallRNA
mosquito
vsiRNA
1 day ago by
ZuelTech
• 0
0
votes
11
replies
316
views
Error Correction with Tadpole and BBMerge
BBmerge
tadpole
error
correction
1 day ago by
Jon
• 0
2
votes
1
reply
97
views
Quantification for small RNAseq data
quantification
seq
data
smallRNA
updated 22 hours ago by
rfran010
★ 1.6k • written 1 day ago by
ZuelTech
• 0
3
votes
3
replies
163
views
GrCh37 or GrCh38? That is the question.
GrCh37
sequence
human
genome
GrCh38
updated 1 day ago by
Pierre Lindenbaum
166k • written 1 day ago by
Anjan
▴ 840
0
votes
2
replies
325
views
Scvi - Integration
integration
singlecell
scvi
written 7 days ago by
t.foskolos
• 0
4
votes
3
replies
229
views
Bootstrapping in RNA-seq
bootstrapping
RNAseq
updated 22 hours ago by
rfran010
★ 1.6k • written 1 day ago by
littlebioinformatician
• 0
0
votes
1
reply
190
views
Computing ka/ks ratio for individual genes.
ks
ka
evolution
selection
updated 1 day ago by
shelkmike
★ 1.6k • written 3 days ago by
Shakunthala Natarajan
• 0
3
votes
5
replies
269
views
Log2FC track Visualization in IGV
visualization
IGV
RNASeq
updated 12 hours ago by
dariober
15k • written 1 day ago by
SomeOne
▴ 210
0
votes
0
replies
153
views
Job:
2-3 Permanent Positions as Bioinformatician/Computational Biologist at Swedish national research infrastructures
Sweden
SciLifeLab
Genomics
Uppsala
Proteomics
1 day ago by
Matthias Zepper
5.1k
2
votes
2
replies
146
views
Obtaining a BED/GTF from Ensembl
rna-seq
ensembl
bcftools
rna
1 day ago by
joe_genome
▴ 60
0
votes
0
replies
100
views
News:
New Bioconductor and Physalia Collaboration!
Bioconductor
DataAnalysis
Genomics
1 day ago by
Physalia-courses
★ 2.6k
1
vote
1
reply
196
views
Read1 and read2 asymmetry in stranded, paired-end rnaseq data aligned by STAR
stranded
STAR
RNAseq
antisense
sense
updated 1 day ago by
rfran010
★ 1.6k • written 2 days ago by
yampolsk
▴ 10
0
votes
1
reply
187
views
Does the order of SplitNCigarReads and MarkDuplicates affect RNA-seq variant calling results?
variantcalling.
rnaseq
gatk
updated 1 day ago by
rfran010
★ 1.6k • written 3 days ago by
iamsmor
• 0
0
votes
0
replies
97
views
Should I standardize age and age2 as covariates in GWAS models?
GWAS
covariates
1 day ago by
yu
• 0
5
votes
6
replies
466
views
Venn Diagram
VennDiagram
updated 17 hours ago by
lieven.sterck
15k • written 4 days ago by
Nasim Gandomdoust
• 0
0
votes
1
reply
147
views
PhageTerm error
phage
genome
phageterm
assamble
updated 1 day ago by
GenoMax
152k • written 2 days ago by
NIkita
• 0
0
votes
1
reply
139
views
WGCNA Workflow from GEO FASTQ Files – Expression Type, Sample Inclusion, and Preprocessing
fastq
wgcna
rna
updated 2 days ago by
GenoMax
152k • written 2 days ago by
tutorwhizzz
• 0
0
votes
0
replies
108
views
small RNA-Seq pipeline Standstill
NGS
miRNA
2 days ago by
anthony.santana.703.j
▴ 30
2
votes
3
replies
232
views
comparison interpretation
model
design
contrast
matrix
11 hours ago by
jkim
▴ 200
0
votes
0
replies
109
views
piRNAs Analysis Pipelines
piRNAs
smallRNA
2 days ago by
GA
• 0
1
vote
1
reply
150
views
Beagle PATH (partially) recognised on Ubuntu 22.04
Ubuntu
Beagle
Beast
MCMC
updated 2 days ago by
GenoMax
152k • written 2 days ago by
Luca Arbore
▴ 10
0
votes
0
replies
132
views
CNV Computation with HoneyBadger
CNV
HoneyBADGER
updated 2 days ago by
GenoMax
152k • written 2 days ago by
mete.han.celebi
• 0
0
votes
0
replies
127
views
How to predict programatically TFBS and calculate PWM Score as JASPAR
PWMScan
TFBS
JASPAR
2 days ago by
t.kajiyama
• 0
0
votes
0
replies
312
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
2 days ago by
ecSeq Bioinformatics
▴ 20
0
votes
14
replies
637
views
Host Removal Issues Human/Dog with samples containing Eukaryotic species
Eukarotic
Mapping
Host
updated 2 days ago by
Mensur Dlakic
★ 29k • written 4 days ago by
Jon
• 0
1
vote
1
reply
228
views
Pharokka Error
error
annotating
viral
pharokka
genome
updated 3 days ago by
Mensur Dlakic
★ 29k • written 3 days ago by
NIkita
• 0
0
votes
0
replies
154
views
Combining Metatranscriptomics (Mtx) and Metagenomics (Mgx)
metagenomics
reference-based
Metatranscriptomics
alignment
updated 3 days ago by
GenoMax
152k • written 3 days ago by
rk009
• 0
1
vote
1
reply
221
views
how to make a circular plot of variants
circular
plot
updated 3 days ago by
Pierre Lindenbaum
166k • written 3 days ago by
analyst
▴ 70
2
votes
6
replies
384
views
GSEA analysis
RNA-seq
RNA
analysis
updated 3 days ago by
GenoMax
152k • written 3 days ago by
Ahmed
• 0
0
votes
0
replies
152
views
how to make go term plot and kegg pathway plot using InterProScan output
interproscan
3 days ago by
analyst
▴ 70
1
vote
3
replies
520
views
Why little difference in RNAseq alignment when flipping forward and reverse strand with paired end reads
mRNA
rna-seq
bowtie
alignment
updated 4 days ago by
swbarnes2
15k • written 4 days ago by
JourneyToAbyss
▴ 250
0
votes
1
reply
240
views
Questions about sample_accession_id and file_accession_id from EGA files
EGA
open
WGS
data
updated 4 days ago by
GenoMax
152k • written 4 days ago by
askif4
▴ 20
4
votes
3
replies
376
views
Example of ClinVar pathogenic variant where the reference allele is pathogenic?
snp
variant
pathogenic
clinvar
updated 4 days ago by
GenoMax
152k • written 5 days ago by
a615ebfb
▴ 60
0
votes
1
reply
258
views
Functional Analysis Using EMU Output – Has Anyone Tried This?
emu
updated 5 days ago by
andres.firrincieli
3.9k • written 5 days ago by
henrique.mouradias
• 0
1
vote
3
replies
330
views
featureCounts -t option not working in v2.0.8?
subread
featureCounts
RNAseq
updated 1 day ago by
rfran010
★ 1.6k • written 5 days ago by
atan
• 0
0
votes
1
reply
265
views
mm10 blacklist regions detailed information
sequencing
DNA
blacklist
updated 5 days ago by
GenoMax
152k • written 5 days ago by
annaA
▴ 10
0
votes
2
replies
303
views
identify unmapped regions
human
illumina
libraries
2 days ago by
María José
▴ 10
0
votes
1
reply
393
views
martCheck - Error - You must provide a valid Mart object - for running HoneyBADGER for CNV computation
CNV
biomaRt
HoneyBADGER
5 days ago by
mete.han.celebi
• 0
0
votes
1
reply
311
views
How to Specify Power Parameter for Adjacency in modulePreservation() (WGCNA)
module
analysis
WGCNA
preservation
updated 5 days ago by
andres.firrincieli
3.9k • written 5 days ago by
Berkan
• 0
0
votes
1
reply
278
views
filters used in mutation discovery from RNAseq data
filter
RNAseq
mutation
updated 5 days ago by
GenoMax
152k • written 5 days ago by
htchd
▴ 20
4
votes
6
replies
503
views
Trouble Using GEO Files with Seurat
seurat
GEO
scRNA
updated 14 hours ago by
antonioggsousa
3.4k • written 6 days ago by
Jamie
• 0
0
votes
0
replies
261
views
Knowledge Graph for AI
KnowledgeGraph
biotech
AI
SPOKE
Bioinformatician
6 days ago by
Cornelio
• 0
121,452 results • Page
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Recent Votes
Comment: DESeq2 design for differential expression with 2 timepoints and 2 controls
Answer: DESeq2 design for differential expression with 2 timepoints and 2 controls
Answer: DESeq2 design for differential expression with 2 timepoints and 2 controls
Comment: unmatched number of reads after trimming treatment by afterqc
A: Number of bases with a certain quality in FASTQ file
A: Peak calling for multiple replicates with Genrich
Answer: DESeq2: error in checkFullRank(modelMatrix)
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Recent Replies
Comment: DESeq2 design for differential expression with 2 timepoints and 2 controls
by
Cristina
• 0
Thanks so much for your response. I had assumed I could test main effects and interactions directly, but now I see how including an interac…
Comment: DESeq2 design for differential expression with 2 timepoints and 2 controls
by
Cristina
• 0
Thank you so much for the clarification! I hadn’t understood that when I read about the design. With the interaction term, the main effects…
Comment: unmatched number of reads after trimming treatment by afterqc
by
德水
• 0
Thank you so much. Fastp works without error.
Comment: Downloading RNAseq datasets from GEO into R
by
Alana
• 0
thank you all
Comment: Downloading RNAseq datasets from GEO into R
by
Alana
• 0
thank you!
Comment: NextSeq 2000 bcl2fastq conversion
by
rds
• 0
In my experience, bcl2fastq works totally fine for NextSeq 2000 data! This error may have been due to a missing/corrupted file or some othe…
Comment: FeatureCount : Successfully assigned alignments is low
by
CFierro
• 0
Are you tried to change the -s option? try with -s 1 or 2 and check the total counts.
Comment: FeatureCount : Successfully assigned alignments is low
by
GenoMax
152k
There are any number of publication that would fit the bill (choosing a random one that does some eval of pipelines) . You can use the data…
Comment: comparison interpretation
by
jkim
▴ 200
Thank you for the explanation!
Comment: Difficulties in calling peaks for CUT&RUN (IgG control with high RPKM value)
by
ATpoint
88k
Can it be that this region is not representative? I mean, at 7-ish million reads you should see sparse IgG at best, because it is basically…
Comment: Log2FC track Visualization in IGV
by
dariober
15k
@SomeOne - if you have found a solution you are happy with, feel free to post it as an answer and mark it as accepted.
Comment: FeatureCount : Successfully assigned alignments is low
by
HarperReed
• 0
Thank you very much for your response. Would you be able to recommend a well-regarded publication or dataset with high-quality RNA-seq dat…
Answer: FeatureCount : Successfully assigned alignments is low
by
ATpoint
88k
From the methods text: > The average RIN was 3.4 There is your answer. The RNA was very poor quality, the libraries mostly consist of (le…
Comment: Trouble Using GEO Files with Seurat
by
antonioggsousa
3.4k
Perhaps the best way to address your issue is to create a new post in this forum with your specific questions, along with the code you’ve u…
Comment: FeatureCount : Successfully assigned alignments is low
by
HarperReed
• 0
thank you for your answer. I made a mistake when copying the link in my previous comment, but the file I actually used is: https://ftp.e…
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