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121,555 results • Page
1 of 2432
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0
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0
replies
40
views
Understanding NCBI vs ENA data
ENA
NCBI
SRA
4 hours ago by
wes
▴ 90
0
votes
0
replies
69
views
News:
Course: Introduction to CRISPR
GenomeEditing
CRISPR
Evolution
13 hours ago by
Physalia-courses
★ 2.6k
1
vote
1
reply
146
views
Best strategy for comparing cell-type composition between disease and healthy groups in single-cell RNA-seq data
Single_cell
updated 14 hours ago by
jared.andrews07
★ 19k • written 16 hours ago by
城玮
• 0
1
vote
4
replies
186
views
RNA-seq assigned alignments
paired-end
STAR
RNA-seq
mapping
single-end
updated 4 hours ago by
jaro.slamecka
▴ 270 • written 18 hours ago by
Manko47
▴ 10
843
votes
170
replies
182k
views
112 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 11 weeks ago by
Biostar
3.6k • written 8.6 years ago by
Istvan Albert
102k
0
votes
1
reply
132
views
Obtain Common SNPS for Mouse Genome
mouse
SNPs
updated 17 hours ago by
GenoMax
152k • written 1 day ago by
joe_genome
▴ 60
1
vote
3
replies
288
views
How do you clean GEO metadata before downstream analysis?
geo
updated 16 hours ago by
yura.grabovska
▴ 800 • written 2 days ago by
Alba
• 0
0
votes
1
reply
141
views
Seeking high-quality curated metabolic models with time-resolved flux data for sonification project
metabolism
sonification
networks
updated 1 day ago by
Mensur Dlakic
★ 29k • written 1 day ago by
omereilam1
• 0
0
votes
0
replies
97
views
Standard way to represent represent indel (insertion or deletion) alleles within a haplotype
haplotypes
indels
haploview
1 day ago by
Mwangana
• 0
1
vote
1
reply
210
views
lovis4u Configuration
graph
lovis4u
genomics
updated 1 day ago by
GenoMax
152k • written 2 days ago by
NIkita
• 0
1
vote
1
reply
225
views
Tool:
Tool to clean GEO metadata
GEO
metadata
updated 1 day ago by
yura.grabovska
▴ 800 • written 2 days ago by
Alba
• 0
1
vote
2
replies
490
views
WGBS Analysis with 1 control sample and 6 disease samples
one
WGBS
sample
updated 2 days ago by
ATpoint
88k • written 13 days ago by
Cassandra
▴ 10
0
votes
2
replies
509
views
How to extract gene list from GEO dataset in R
coding
beginner
question
r
updated 2 days ago by
Shohel
• 0 • written 13 days ago by
decorus
• 0
0
votes
6
replies
450
views
RNA seq strandedness (reverse-strand)
seq
reverse-stranded
strand
RNA
1 day ago by
ZuelTech
• 0
0
votes
0
replies
168
views
TFs and enrichment analysis for TRAP sequencing
TRAP
3 days ago by
Genesis
• 0
0
votes
2
replies
260
views
Extract track data from "search by region" feature on ENCODE
Encode
21 hours ago by
AlienPumpkinPie
• 0
9
votes
8
replies
936
views
Weird p-value distribution on edgeR results
edgeR
pvalue-distribution
gene-expression
updated 3 days ago by
dariober
15k • written 11 days ago by
Guillermo
▴ 30
1
vote
3
replies
296
views
Draw GO tree for some GO ids with coloring
enrichment
GO
3 days ago by
boczniak767
▴ 880
2
votes
4
replies
2.6k
views
Extract transcript fasta using gff
fasta
gff
updated 3 days ago by
cmdcolin
★ 4.2k • written 4.1 years ago by
boczniak767
▴ 880
0
votes
0
replies
185
views
Understanding MAG completeness and contig composition in metagenomic bins
data
shotgun
3 days ago by
shevch2009
▴ 20
1
vote
4
replies
1.1k
views
Problem with Mirdeep2 and Randfold output
mirdeep2
Randfold
updated 3 days ago by
Jasim
• 0 • written 15 months ago by
otieno43
▴ 40
0
votes
1
reply
244
views
calculating coverage of gene in my metagenomes with samtools
samtools
depth
metagenome
coverage
updated 3 days ago by
Pierre Lindenbaum
166k • written 4 days ago by
lintonf
• 0
1
vote
1
reply
240
views
how to merge gbz files
vg
updated 4 days ago by
Jouni Sirén
▴ 680 • written 4 days ago by
lushjia
• 0
2
votes
1
reply
240
views
plotting read length distribution of Single End data
read_length_distribution
single_end_sequencing
WGS
4 days ago by
Meghan.T
▴ 10
4
votes
1
reply
289
views
Preranked GSEA permutation
GSEA
updated 4 days ago by
ATpoint
88k • written 5 days ago by
as823jk
• 0
1
vote
2
replies
370
views
why bwa-mem only return one read with pair-read end
sequencing
bwa-mem
updated 2 days ago by
rfran010
★ 1.6k • written 4 days ago by
QX
▴ 70
0
votes
1
reply
227
views
Identification problem of IDE-8 cell on culture with inverted microscope
IDE-8
updated 4 days ago by
rfran010
★ 1.6k • written 4 days ago by
Prashanta
• 0
0
votes
2
replies
356
views
Identifying RBP motifs overlapping exons
motifs
bedtools
RBP
updated 4 days ago by
GenoMax
152k • written 7 days ago by
RK
• 0
0
votes
0
replies
196
views
News:
Upcoming NGS Data Analysis Courses 2025
SingleCell
RNAseq
Epigenomics
Illumina
DNAseq
4 days ago by
ecSeq Bioinformatics
▴ 20
0
votes
1
reply
262
views
How to match clinical information with expression data in R
R
updated 4 days ago by
Arup Ghosh
3.3k • written 4 days ago by
py3296746920
• 0
3
votes
1
reply
442
views
Identify SNP, Indel variants from a List of FASTA sequence
SNP
updated 5 days ago by
Mark
★ 1.7k • written 9 days ago by
Trinh
▴ 10
2
votes
15
replies
941
views
Which Reference Hg38 or T2T?? Both??
Host
Removal
5 days ago by
Jon
• 0
3
votes
2
replies
331
views
Can I transduce HEK293T with Cas9 lentivirus followed by transfection with sgRNAs?
lentivirus
Transduction
CRISPR
transfection
offtopic
updated 5 days ago by
jared.andrews07
★ 19k • written 5 days ago by
louisflower1999
• 0
3
votes
3
replies
400
views
Mitochondrial annotation tool for algae
barcoding
annotation
updated 5 days ago by
Juke34
9.3k • written 5 days ago by
firefox91
• 0
1
vote
2
replies
358
views
Identifying gene outliers in a genome using composition analysis.
RSCU
composition
GC
outliers
updated 5 days ago by
GenoMax
152k • written 5 days ago by
Shakunthala Natarajan
• 0
1
vote
5
replies
455
views
Mapping to a template sequece
sequencing
4 days ago by
QX
▴ 70
0
votes
2
replies
393
views
quality control for 16s metagenome reads
quality
metagneome
control
16s
fastp
updated 5 days ago by
GenoMax
152k • written 7 days ago by
m90
▴ 30
0
votes
2
replies
385
views
Loss of strandedness in the Illumina Strandedness Total RNA protocol
Illumina
RNA-seq
reads
stranded
updated 6 days ago by
ATpoint
88k • written 6 days ago by
Anjan
▴ 840
0
votes
1
reply
365
views
Help using ShinyCell2 and Seurat v5 object.
shinycell
seurat
shiny
shinycell2
scRNA
updated 5 days ago by
antonioggsousa
3.4k • written 6 days ago by
Jamie
• 0
0
votes
0
replies
261
views
News:
Machine Learning for Multi-Omics Integration at the University of Barcelona– Dec 2025
Machine-Learning
Sulti-Omics
Depp-Learning
Data-Integration
BigData
6 days ago by
Physalia-courses
★ 2.6k
0
votes
0
replies
281
views
Compare alternative splicing patterns between human and mouse?
orthologs
rna-seq
splicing
alternative
6 days ago by
aboll
▴ 20
2
votes
6
replies
534
views
Trouble getting representatives from clustered_nr database
database
blast
4 days ago by
Adolfo
• 0
0
votes
0
replies
260
views
FindTransferAnchors (reference prediction) vs Manual Annotations
Seurat
6 days ago by
reddyornah
• 0
3
votes
4
replies
468
views
NCBI Datasets CLI Question
ncbi-datasets
7 days ago by
Bjorn
• 0
0
votes
0
replies
282
views
Incomplete assembly in HPRC dataset
pangenome
HPRC
reference
7 days ago by
ohell
• 0
4
votes
3
replies
446
views
Joint Calling for Large Germline WGS Cohort
NGS
RAM
cohort
Genomics
WGS
updated 7 days ago by
Jeremy Leipzig
23k • written 7 days ago by
j.k3096
▴ 20
2
votes
4
replies
470
views
how shoud the phred score be intepreted?
sequencing
updated 7 days ago by
GenoMax
152k • written 7 days ago by
QX
▴ 70
0
votes
3
replies
545
views
Inherited pipeline uses RNA-seq variant calls for WASP filtering—shouldn’t it be external SNPs?
WASP
updated 6 days ago by
i.sudbery
21k • written 10 days ago by
jonas.andersson
▴ 40
0
votes
0
replies
291
views
WGCNA analysis for Proteomics data
Proteomics
WGCNA
7 days ago by
Sumit Paliwal
▴ 40
3
votes
8
replies
6.8k
views
7 follow
Cellranger count pipestance failed: The read lengths are incompatible with all the chemistries
10x
cellranger
single-cell
updated 7 days ago by
zhang
• 0 • written 3.1 years ago by
firestar
★ 1.7k
121,555 results • Page
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Recent Votes
Answer: Best strategy for comparing cell-type composition between disease and healthy gr
WGBS Analysis with 1 control sample and 6 disease samples
C: Calculating the expression level of genes regarding central tendenties
A: Why you shouldn't normalize count data using gene-length AND library size for co
C: Handling replicates in Chip-seq
Comment: lovis4u Confiduration
Answer: RNA-seq assigned alignments
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Recent Replies
Comment: RNA-seq assigned alignments
by
jaro.slamecka
▴ 270
To reiterate one of GenoMax's questions, is the new sequencing provider making the libraries for you? If so, have they by any chance used r…
Answer: Best strategy for comparing cell-type composition between disease and healthy gr
by
jared.andrews07
★ 19k
I'd recommend reading the [differential abundance testing chapter](https://bioconductor.org/books/3.21/OSCA.multisample/differential-abunda…
Comment: How do you clean GEO metadata before downstream analysis?
by
yura.grabovska
▴ 800
They did make a [Tool post originally](https://www.biostars.org/p/9613596), but still phrased it as something they just came across rather …
Comment: How do you clean GEO metadata before downstream analysis?
by
jared.andrews07
★ 19k
Agreed, just make a "Tool" post if you want to spread the word about it. People tend to take those much better than these weak attempts at…
Comment: RNA-seq assigned alignments
by
GenoMax
152k
Since you have decided to move to a new sequence provider that decision is for economic reasons and not scientific, so not much to think ab…
Comment: Obtain Common SNPS for Mouse Genome
by
GenoMax
152k
These are multi-strain VCF's so you could look for SNP's common across the strains (see --> https://www.biostars.org/p/9498113/ ) . Keep in…
Comment: RNA-seq assigned alignments
by
Manko47
▴ 10
>Are you comparing the same exact library sequenced by two different companies. Nah it's just majorty of my old datasets osciliated around…
Answer: RNA-seq assigned alignments
by
GenoMax
152k
> Previously on the single-end data from old company I was getting around 50-60% of the uniquely aligned reads Are you comparing the same…
Comment: Extract track data from "search by region" feature on ENCODE
by
AlienPumpkinPie
• 0
Thank you for your reply! Yeah I thought the same. It feels weird to me that this is not an obvious feature.
Comment: How do you clean GEO metadata before downstream analysis?
by
yura.grabovska
▴ 800
Again... "I recently *stumbled* upon a small browser-based tool" On the site: "Created by alba0gf" That's the second time you've linked y…
Comment: Tool to clean GEO metadata
by
yura.grabovska
▴ 800
"i recently *found* this simple tool" Go to site "Created by alba0gf" I mean... why lie?
Comment: DGE analysis in Seurat using paired samples per donor ?
by
yura.grabovska
▴ 800
What do you think you'll gain by doing tumour vs normal at single-cell resolution? The whole point of single cell is to define sub-populati…
Comment: RNA seq strandedness (reverse-strand)
by
ZuelTech
• 0
My purpose is to count reads mapping to the genomes. Was my code above in doing so correct?
Comment: Seeking high-quality curated metabolic models with time-resolved flux data for s
by
Mensur Dlakic
★ 29k
Maybe this will work, minus the flux data. https://www.kegg.jp/kegg/pathway.html
Comment: lovis4u Confiduration
by
GenoMax
152k
Unless you are able to use "user defined window" with color (as noted in https://art-egorov.github.io/lovis4u/ExampleDrivenGuide/cmd_guide/…
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