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120,421 results • Page
1 of 2409
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Votes
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0
votes
0
replies
10
views
Why are phenotype values missing in PLINK analysis despite no NA values in the input?
PLINK
PRS
PHS
PGS
SNPanalysis
1 hour ago by
comu
• 0
2
votes
2
replies
148
views
Should I not have any adapters after trimming?
RNA-seq
updated 7 hours ago by
swbarnes2
14k • written 1 day ago by
bioinfo
▴ 150
1
vote
3
replies
172
views
Multiple fail points in fastqc file
fastqc
report
updated 7 hours ago by
swbarnes2
14k • written 1 day ago by
dr.deepakkukkar
• 0
0
votes
3
replies
151
views
Incorrect gene naming (SYMBOL)
Gene-annotation
updated 9 hours ago by
Alex Reynolds
36k • written 19 hours ago by
Biomed-jeh
▴ 70
0
votes
0
replies
89
views
Interactive UMAP for scRNA-seq Data
HTML
RMarkdown
Interactive-UMAP
scRNA-seq
updated 15 hours ago by
Ram
44k • written 16 hours ago by
s
• 0
828
votes
169
replies
166k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 4 months ago by
Biostar
3.4k • written 8.2 years ago by
Istvan Albert
102k
1
vote
1
reply
161
views
Problem after subset of single cell integrated dataset in seurat using sctransform
seurat
integration
scRNAseq
sctransform
subset
20 hours ago by
NGS_enthusiast
• 0
3
votes
4
replies
234
views
Per Sequence GC Content fail
fastqc
updated 1 day ago by
GenoMax
149k • written 1 day ago by
Eduardo
• 0
2
votes
4
replies
307
views
Compare genomes of different species and published studies (different years, sequencing technologies...) is correct?
comparative-genomics
11 hours ago by
Bruno
• 0
2
votes
1
reply
173
views
Why do people say it doesn't matter whether you run unassembled or assembled reads through Kraken?
assembly
unassembled-reads
Kraken
updated 21 hours ago by
dthorbur
★ 2.8k • written 1 day ago by
trkfs
▴ 10
3
votes
5
replies
190
views
Best way to provide sequences to Local Colabfold to not overload their mmseq2 server
Local
ColabFold
updated 20 hours ago by
dthorbur
★ 2.8k • written 1 day ago by
myoui3122010
▴ 30
4
votes
9
replies
310
views
Preventing Conda/Mamba from accessing Anaconda repos when institution blocks them
conda
mamba
repos
miniforge
channels
9 hours ago by
kalavattam
▴ 310
3
votes
6
replies
880
views
Tool:
A c library for reading and writing sequences in fasta and fastq format.
seqio
1 day ago by
dwpeng
▴ 110
0
votes
0
replies
82
views
Difference between mutect2 and strelka2
mutect2
strelka2
1 day ago by
ramiro.barrantes
▴ 20
0
votes
1
reply
209
views
GO Analysis Combine or Separate DEGs
clusterProfiler
GO
updated 1 day ago by
mark.ziemann
★ 2.0k • written 3 days ago by
Koki
• 0
1
vote
1
reply
269
views
scType on Xenium Spatial Transcriptomics
Spatial
Xenium
scType
updated 1 day ago by
geno89
▴ 10 • written 15 days ago by
Emma Jayne
▴ 10
0
votes
0
replies
91
views
How to extract the components of a cluster after pheatmap
Heatmap
Export
Cluster
1 day ago by
Luiza
• 0
0
votes
1
reply
395
views
Interpretation of MSMC2/PSMC/betaPSMC/ngsPSMC
Demography
PSMC
MSMC
updated 1 day ago by
csarabia
• 0 • written 3 months ago by
vap768
• 0
0
votes
3
replies
184
views
Metagenomic binnig step
binnig
tools
Metagenomics
updated 1 day ago by
Mensur Dlakic
★ 28k • written 1 day ago by
m90
▴ 30
0
votes
1
reply
126
views
Tool to phase genotyped large SV from short-read data?
sv
structural
variant
short-reads
haplotype
phasing
updated 23 hours ago by
Pierre Lindenbaum
165k • written 1 day ago by
afurches
• 0
0
votes
0
replies
82
views
Normalisation for sample splice junction profiles
splicing
normalisation
RNAseq
1 day ago by
coolmattmonkey
• 0
0
votes
0
replies
84
views
Calculate base pair probability differences between Wild type and mutant sequences
probabilities
rnaplfold
rnafold
basepair
1 day ago by
RK
• 0
0
votes
1
reply
231
views
What is indicated by the red dotted lines in the `tiny_10x_pbmc.pdf` out put from `cellbender remove-background`
remove-background
cellbender
updated 19 hours ago by
Bastien Hervé
6.1k • written 1 day ago by
joshua.theisen
▴ 30
1
vote
2
replies
220
views
Parameters for annotation with maker
Maker
masking
plant
annotation
16 hours ago by
san96
▴ 170
3
votes
3
replies
173
views
Extracting Sequences from a FASTA File Using Exon Coordinates from a GTF File
gtf
fasta
updated 1 day ago by
colindaven
7.1k • written 1 day ago by
Milica
• 0
0
votes
2
replies
150
views
Low Read Mapping for Differentially Expressed Genes in 3' RNA-seq Analysis
gene-expression
single-end
RNA-seq
updated 1 day ago by
Ram
44k • written 1 day ago by
Emy Alade
• 0
2
votes
3
replies
172
views
mapDamage error
mapDamage
1000genomes
1 day ago by
anna.utili
• 0
0
votes
0
replies
99
views
News:
Online Course: Flow Cytometry Data Analysis with R/Bioconductor (17–20 March 2025)
R
Bioconductor
Flow-Cytometry
Cancer-Genomics
1 day ago by
Physalia-courses
★ 2.6k
2
votes
1
reply
150
views
Average length of mRNA on NCBI annotation seems too high
mRNA
updated 1 day ago by
lieven.sterck
15k • written 2 days ago by
yh1126
• 0
0
votes
0
replies
100
views
How to normalize qPCR results for covariates like cell type markers
Normalization
qPCR
RNA-Seq
1 day ago by
Sara
▴ 40
0
votes
4
replies
279
views
Proteomics Data Analysis
Proteomics
updated 1 day ago by
ATpoint
86k • written 2 days ago by
frarodmar17
• 0
0
votes
0
replies
126
views
Demultiplexing asymmetrically barcoded reads from multiplex amplicon nanopore sequencing
ONT
demultiplex
2 days ago by
michael.flower.14
▴ 200
6
votes
8
replies
371
views
Regex in umi-tools doesn't identify pattern in non-beginning positions
whitelist
UMI-Tools
UMI
UMI-TOOLS
umi-tools
1 day ago by
kalaivani
▴ 10
1
vote
1
reply
188
views
GRCh38 reference paths in human pangenome
HPRC
GRCh38
updated 1 day ago by
cmdcolin
★ 4.1k • written 2 days ago by
Rugare
• 0
2
votes
1
reply
174
views
Annotate WGS VCF with Allele Frequencies
snpeff
vcf
wgs
allele
updated 2 days ago by
Pierre Lindenbaum
165k • written 2 days ago by
Gabriel
• 0
1
vote
4
replies
267
views
dentifying tumor vs normal cells in spatial transcriptomics
seurat
xenium
spatial-transcriptomics
1 day ago by
geno89
▴ 10
2
votes
2
replies
875
views
Which zUMIs output to use for differential gene expression?
zumis
rnaseq
smartseq3
single-cell
updated 1 day ago by
dsull
★ 7.2k • written 18 months ago by
firestar
★ 1.6k
0
votes
1
reply
143
views
build a diploid reference using cactus-pangenome pipeline
cactus
pangenome
diploid
graph
vg
updated 2 days ago by
Dunois
★ 2.9k • written 2 days ago by
lucianocalderon
▴ 10
0
votes
1
reply
173
views
Bowtie index size / richness matters ?
bowtie
updated 2 days ago by
colindaven
7.1k • written 2 days ago by
maschi88
• 0
1
vote
0
replies
131
views
VEP doesn't count CADD
CADD
VEP
annotation
2 days ago by
balanannie
▴ 10
6
votes
9
replies
5.2k
views
6 follow
News:
New in DiffBind: dba.plotProfile() - Peak profiles and profile heatmaps
DiffBind
ChIP-seq
deepTools
visualization
ATAC-seq
updated 2 days ago by
lijiangres
• 0 • written 3.7 years ago by
Rory Stark
★ 2.1k
2
votes
1
reply
181
views
Per tile sequence fails after trimming
fastQC
WES
Sequencing
updated 2 days ago by
GenoMax
149k • written 2 days ago by
ijarne
▴ 20
1
vote
4
replies
821
views
CIBERSORTx error (error in rep(2, size * length(cells) -1)) : invalid 'times' argument
deconvolution
RNA-seq
CIBERSORTx
CIBERSORT
updated 3 days ago by
zhbyrd
• 0 • written 8 months ago by
Mr. George
▴ 10
0
votes
0
replies
180
views
Pipelines/Tools for cleaning UK Biobank data?
UKBiobank
RAP
3 days ago by
Christian
• 0
0
votes
0
replies
166
views
Key error when using prepDE.py
python
prepDE
stringtie
keyerror
updated 2 days ago by
WouterDeCoster
47k • written 3 days ago by
mohamadelian1996
• 0
1
vote
2
replies
268
views
How to use harmony with scanpy?
scanpy
harmony
3 days ago by
bioinfo
▴ 150
0
votes
2
replies
231
views
Scdblfinder issue
R
scdblfinder
updated 3 days ago by
Ram
44k • written 3 days ago by
rahma.khoualdia
• 0
0
votes
0
replies
169
views
Repeat Modeler Database Generation
repeat_modeler
repeats
fungi
annotation
genomes
3 days ago by
SomeOne
▴ 170
0
votes
2
replies
230
views
Merging paired-end reads after featureCounts
featureCounts
RNAseq
updated 3 days ago by
ATpoint
86k • written 3 days ago by
n_navy
• 0
1
vote
3
replies
301
views
Proteomics DEA
Proteomics
updated 1 day ago by
ATpoint
86k • written 3 days ago by
frarodmar17
• 0
120,421 results • Page
1 of 2409
Recent Votes
Answer: Should I not have any adapters after trimming?
Answer: Per Sequence GC Content fail
Why do people say it doesn't matter whether you run unassembled or assembled reads through Kraken?
Comment: Compare genomes of different species and published studies (different years, seq
Comment: Compare genomes of different species and published studies (different years, seq
Should and can we use the new draft pangenome reference?
Answer: Should I not have any adapters after trimming?
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Recent Replies
Answer: Should I not have any adapters after trimming?
by
swbarnes2
14k
Kallisto, or aligners like STAR won't care. STAR for sure is happy to soft-clip reads to make the alignment happen. So if there's enough …
Answer: Multiple fail points in fastqc file
by
swbarnes2
14k
No one can comment intelligently on this **without knowing what it is**. No one can understand what these graphs mean without the context …
Answer: Incorrect gene naming (SYMBOL)
by
Alex Reynolds
36k
> A quick solution I thought of is to write code that removes _1 from any gene name. However, I’m unsure whether _1 is ever part of a real …
Comment: Compare genomes of different species and published studies (different years, seq
by
Bruno
• 0
The same in dthorbur answer.
Comment: Compare genomes of different species and published studies (different years, seq
by
Bruno
• 0
I'm new with genomics, I always deal only with molecular evolutionary studies involvieng few genes. So in these cases, I took tens of diffe…
Comment: Preventing Conda/Mamba from accessing Anaconda repos when institution blocks the
by
kalavattam
▴ 310
Thank you for this suggestion. However, @genomax is correct: Access is "blocked at the level of main institutional firewall."
Comment: Per Sequence GC Content fail
by
Mensur Dlakic
★ 28k
Hopefully it is clear that your GC-plot is similar to the one I posted. Nothing was wrong with my dataset and it is likely that your datase…
Comment: Incorrect gene naming (SYMBOL)
by
Ram
44k
`_1` is not a part of any gene symbol as far as I'm aware. It is possible that some piece of software along the way chose to address duplic…
Comment: Incorrect gene naming (SYMBOL)
by
Ram
44k
Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the cod…
Comment: Preventing Conda/Mamba from accessing Anaconda repos when institution blocks the
by
GenoMax
149k
OP is likely not in a position to run a personal proxy server. Access may be blocked at the level of main institutional firewall (more than…
Comment: Compare genomes of different species and published studies (different years, seq
by
GenoMax
149k
> I want to conduct a study using genomes deposited in databases And what do you hope to get out of such a study? > Is it possible to do…
Comment: Preventing Conda/Mamba from accessing Anaconda repos when institution blocks the
by
Jesse
▴ 850
I wonder (since I haven't actually tried it for this) if [bouncing your anaconda.org requests through a proxy](https://docs.conda.io/projec…
Comment: Parameters for annotation with maker
by
san96
▴ 170
Hi @colindaven , Thanks for your reply, the problem I have is actually about how to configure my make_opts file for my first round. My pla…
Comment: Preventing Conda/Mamba from accessing Anaconda repos when institution blocks the
by
kalavattam
▴ 310
With `channel_priority: strict` or `channel_priority: flexible`, I continue to encounter the same issue: ``` Download error (35) SSL connec…
Comment: Compare genomes of different species and published studies (different years, seq
by
dthorbur
★ 2.8k
This is a very broad question, and the answer depends on what you aim to get out of it. Yes, you can certainly conduct a comparative analys…
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