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122,229 results • Page
1 of 2445
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News:
Upcoming Ensembl API and data access changes - new blog post available
Ensembl
just now by
Ensembl Outreach
• 0
0
votes
0
replies
49
views
News:
Spatial Transcriptomics course
SpatialTranscriptomics
singlecell
Bioconductor
R
5 hours ago by
Physalia-courses
★ 2.7k
2
votes
2
replies
132
views
Re-assembling old RNA-seq reads vs. using an existing transcriptome assembly
non-model-organism
de-novo-assembly
RNA-seq
updated 5 hours ago by
GenoMax
154k • written 8 hours ago by
Mostafa
• 0
852
votes
173
replies
221k
views
113 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
handbook
training
updated 6 weeks ago by
Biostar
3.7k • written 9.0 years ago by
Istvan Albert
103k
0
votes
0
replies
64
views
RNA-seq: identifying pericentromeric region
genomics
transcriptomics
rna-seq
assembly
aligning
7 hours ago by
Polly
• 0
0
votes
1
reply
84
views
"sortmerna" quitting early--is this is a memory issue?
sortmerna
RNA-seq
updated 8 hours ago by
colindaven
8.1k • written 8 hours ago by
Andrew
• 0
0
votes
1
reply
292
views
Power calculations for differentially methylated DNA samples from sequencing
methylation
updated 8 hours ago by
colindaven
8.1k • written 5 days ago by
graeme.thorn
▴ 110
0
votes
4
replies
260
views
Data integration single cell using Harmony
singlecell
10x
Harmony
dataIntegration
9 hours ago by
_deb
• 0
1
vote
1
reply
137
views
mapping sequences on specific region of bacteria genome
genome
fastq
mapping
updated 17 hours ago by
samuel.a.odonnell
▴ 650 • written 18 hours ago by
cabraham03
▴ 30
3
votes
5
replies
5.8k
views
Prokka output genes clusterization by function
data
prokka
shotgun
updated 17 hours ago by
Mensur Dlakic
★ 30k • written 11 weeks ago by
shevch2009
▴ 20
0
votes
1
reply
413
views
Manual corrections for allele mismatches
mismatch
harmonisation
PRS
updated 20 hours ago by
curious
▴ 900 • written 9 days ago by
Sakshi
• 0
0
votes
0
replies
80
views
News:
Workshop: Virtual RAD-seq, December 16–18
genomics
RADseq
bioinformatics
workshop
UConn
23 hours ago by
zsc25001
▴ 10
0
votes
3
replies
208
views
Basics of WGCNA
WGCNA
updated 23 hours ago by
pinheirofabiano
▴ 130 • written 1 day ago by
brooke.bell1299
• 0
1
vote
2
replies
181
views
Repeated Coordinate Errors (>171823) in NC_007605.1 (EBV) GTF Conversion (LMP2A/2B Exons)
cellranger
updated 1 day ago by
GenoMax
154k • written 1 day ago by
halo22
▴ 300
1
vote
1
reply
125
views
combining RNA-seq replicates from low and deep-seq - is it useful?
biostats
depth
RNA-seq
updated 1 day ago by
GenoMax
154k • written 1 day ago by
michaelp
• 0
0
votes
8
replies
778
views
Issue while running Kenddata.
paired
Kenddata
fastq
16 hours ago by
rana.elromh
• 0
3
votes
3
replies
308
views
dismatch between pyOMADB and the website ?
OMA
PYOMADB
updated 1 day ago by
Adrian Altenhoff
★ 1.2k • written 2 days ago by
CH
• 0
2
votes
2
replies
979
views
Generating a Python parsable local db from dbSNP
Python
1 day ago by
gernophil
▴ 130
0
votes
1
reply
305
views
Confusion about which docking pose to visualize vs. which pose to use for binding energy
zinc
autodockZn
docking
updated 1 day ago by
dthorbur
★ 3.2k • written 5 days ago by
Ria
• 0
0
votes
2
replies
181
views
How to identify WES source tissue (blood vs. other)
WES
1 day ago by
gernophil
▴ 130
1
vote
1
reply
173
views
STAR genome index generation: NF-core vs manual parameters (seeking clarification)
transcriptome
R
coding
updated 1 day ago by
Pierre Lindenbaum
166k • written 1 day ago by
Amb@r85
▴ 10
4
votes
3
replies
590
views
How to perform GO enrichment in non-model organisms?
GO
updated 1 day ago by
lieven.sterck
16k • written 4 days ago by
CaERu
• 0
0
votes
0
replies
218
views
ARACNe-AP to viper aracne2regulon error
VIPER
R
ARACNe-AP
aracne2regulon
package
updated 4 days ago by
GenoMax
154k • written 4 days ago by
thasweer
• 0
0
votes
0
replies
219
views
News:
online course - Epigenomics Data Analysis
HIC
ATACseq
Epigenomics
Chipseq
MultiOmics
4 days ago by
Physalia-courses
★ 2.7k
4
votes
2
replies
736
views
How excactly is the Q30 is calculated?
Q30
MGI
updated 4 days ago by
colindaven
8.1k • written 5 days ago by
rodrigo
• 0
0
votes
0
replies
380
views
ClinVar - how can a missense coding variant in a gene also be a variant on a non coding antisense RNA gene?
Clinvar
transcripts
variants
4 days ago by
hello_bioinf
▴ 250
0
votes
1
reply
486
views
Question about QC and scrublet
scrublet
updated 4 days ago by
Arup Ghosh
3.5k • written 5 days ago by
biotrekker
▴ 110
2
votes
2
replies
668
views
circos plot for genomic features
bed
R
plot
track
circos
4 days ago by
Matteo Ungaro
▴ 140
0
votes
0
replies
235
views
News:
Advanced Python for Biologists
Python
updated 4 days ago by
GenoMax
154k • written 5 days ago by
oliverhooker
▴ 110
0
votes
0
replies
225
views
News:
Python for Biological Data Exploration & Visualisation
Python
updated 4 days ago by
GenoMax
154k • written 5 days ago by
oliverhooker
▴ 110
0
votes
0
replies
235
views
News:
Single-Cell RNA-Seq Analysis
Single
RNA-seq
cell
updated 4 days ago by
GenoMax
154k • written 5 days ago by
oliverhooker
▴ 110
0
votes
0
replies
223
views
News:
Deep Learning Using Python
Python
Learning
Deep
updated 4 days ago by
GenoMax
154k • written 5 days ago by
oliverhooker
▴ 110
0
votes
0
replies
221
views
News:
Python for Data Science & Statistical Computing
Python
updated 4 days ago by
GenoMax
154k • written 5 days ago by
oliverhooker
▴ 110
1
vote
2
replies
607
views
Chip-seq analysis Diffbind
Chipseq
Diffbind
40 minutes ago by
Irene
▴ 10
2
votes
3
replies
1.3k
views
strong appearing variant not found by haplotypecaller in -ERC mode and deepvariant but with haplotypecaller in normal mode
deepvariant
haplotypecaller
6 days ago by
thomas.heigl.ibk
▴ 20
0
votes
0
replies
267
views
News:
online course Introduction to Machine Learning with R (5th edition)
R
AI
omics
Genomics
MachineLearning
6 days ago by
Physalia-courses
★ 2.7k
3
votes
5
replies
1.8k
views
low quality data or file name swapping -- cellranger arc errors when processing 10x scMultiomics data
scMultiomics
ENCODE
scRNA-seq
scATAC-seq
cellranger-arc
updated 5 days ago by
Arup Ghosh
3.5k • written 6 days ago by
Wu-Sheng Zhang
▴ 10
1
vote
3
replies
3.1k
views
The geo samples is not having sentrix id and sentrix position. But this information is needed for RnBeads workflow. How to proceed?
R
next-gen
sequencing
updated 7 days ago by
yura.grabovska
▴ 890 • written 8.1 years ago by
preethibagopi28
▴ 10
0
votes
2
replies
978
views
Finding Sentrix ID in HM450K arrays
Methylarray
updated 7 days ago by
yura.grabovska
▴ 890 • written 12 days ago by
Betul
• 0
6
votes
3
replies
848
views
Can i use orthofinder for small protein datasets and not full proteome?
orthofinder
effectors
6 days ago by
alexandrakortsi
• 0
0
votes
1
reply
421
views
How to improving 2-Nucleotide RNA-seq Mapping Accuracy
base-conversion
7 days ago by
2411110159
• 0
59
votes
31
replies
17k
views
13 follow
Tutorial:
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation
meta
how-to
updated 7 days ago by
2411110159
• 0 • written 9.8 years ago by
Ram
45k
5
votes
8
replies
1.9k
views
ID unifiying across different datasets
UniProt
GeneSymbole
ID
updated 5 days ago by
GenoMax
154k • written 7 days ago by
zizigolu
★ 4.4k
4
votes
6
replies
3.7k
views
Visualize methylation status in Pacbio Hifi read
Pacbio
methylation
updated 5 days ago by
cmdcolin
★ 4.4k • written 2.4 years ago by
Cathy
▴ 10
1
vote
2
replies
532
views
direct RNA long-reads alignment against reference genome
nanopore
sequencing
7 days ago by
frarodmar17
• 0
0
votes
0
replies
286
views
News:
GWAS course - online, January 2026
R
Link
Imputation
GWAS
7 days ago by
Physalia-courses
★ 2.7k
0
votes
1
reply
1.5k
views
Bumphunter function in minfi
minfi
methylation
DMR
bumphunter
R
updated 7 days ago by
jxinyi118
• 0 • written 2.7 years ago by
eebloom
▴ 110
2
votes
2
replies
771
views
snpEff: Unsupported structural variant types
vcf
snpEff
6 days ago by
shpak.max
▴ 70
1
vote
1
reply
865
views
How to pull specific comparisons for DEGs in DESeq2? Trying to understand setting contrasts after the model matrix and results lists.
DEG
RNAseq
DESeq2
updated 7 days ago by
ATpoint
90k • written 8 days ago by
atan
• 0
4
votes
4
replies
1.0k
views
Feature Counts vs Salmon quantification
FEATURECOUNTS
SALMON
RNA-Seq
STAR
updated 8 days ago by
GenoMax
154k • written 8 days ago by
rajdeepboral00
▴ 70
122,229 results • Page
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Recent Votes
Answer: Chip-seq analysis Diffbind
Question about variant calling method using pangenome-graph
Comment: SyntaxError in file /snakefile, line 22: invalid decimal literal: None
Answer: Is this Rosalind inspired project actually useful?
Answer: Minimap2 segfaults when mapping Nanopore reads to a very large reference databas
Comment: How to normalize the intensity of bigwig files based on a group of house-keeping
Answer: Re-assembling old RNA-seq reads vs. using an existing transcriptome assembly
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Recent Replies
Comment: Chip-seq analysis Diffbind
by
Irene
▴ 10
Thank you very much for always answering my doubts and questions. I truly value and appreciate it because it helps me understand the result…
Comment: Minimap2 segfaults when mapping Nanopore reads to a very large reference databas
by
firefox91
▴ 10
Many thanks !
Answer: Re-assembling old RNA-seq reads vs. using an existing transcriptome assembly
by
GenoMax
154k
> I have access to both the raw reads and the previously assembled transcriptome submitted to TSA. and > I am trying to determine wheth…
Answer: Re-assembling old RNA-seq reads vs. using an existing transcriptome assembly
by
dthorbur
★ 3.2k
There are a few factors to consider: **The quality of the existing reference.** If there is a high quality chromosome level assembly,…
Comment: "sortmerna" quitting early--is this is a memory issue?
by
colindaven
8.1k
Pls add the output and your system (especially RAM), no one here can guess.
Answer: Power calculations for differentially methylated DNA samples from sequencing
by
colindaven
8.1k
There are software packages for power analysis such as https://academic.oup.com/bioinformaticsadvances/article/5/1/vbaf150/8173951.
Comment: Data integration single cell using Harmony
by
Arup Ghosh
3.5k
Run QC for each sample separately, then merge run SCTransform, PCA, then Harmony, UMAP, FindNeighbors and FindClusters.
Comment: Data integration single cell using Harmony
by
_deb
• 0
Thank you for the quick answer. I still have a doubt. It would be better to pre-process each sample separately (*filtering, SCTransform…
Comment: Issue while running Kenddata.
by
rana.elromh
• 0
I checked the memory before executing this command. I made a bash script on Ubuntu to run it on 15 folders. But, this problem happened in f…
Comment: Prokka output genes clusterization by function
by
Mensur Dlakic
★ 30k
Many proteins have multiple domains, and are correctly classified with multiple KO numbers. That's not a bug in `kofam_scan` but rather a r…
Comment: mapping sequences on specific region of bacteria genome
by
samuel.a.odonnell
▴ 650
If you want to visualise the mapping; take a look at using IGV. It just requires the genome you used to map the reads and the BAM output (n…
Comment: Prokka output genes clusterization by function
by
shevch2009
▴ 20
Thanks, I had completely forgotten that METABOLIC works with protein sequences. That will work :) I was just trying to figure out how peop…
Answer: Prokka output genes clusterization by function
by
Mensur Dlakic
★ 30k
It is easy to install `kofam_scan` and get the output: https://github.com/takaram/kofam_scan What is the impediment to using METABOLI…
Answer: Manual corrections for allele mismatches
by
curious
▴ 900
take a look at thomas winkler's stuff: https://www.nature.com/articles/nprot.2014.071
Comment: Repeated Coordinate Errors (>171823) in NC_007605.1 (EBV) GTF Conversion (LMP2A/
by
halo22
▴ 300
Thanks for sharing this. I was able to get makeref to work.
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