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121,552 results • Page
1 of 2432
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1
vote
3
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58
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RNA-seq assigned alignments
paired-end
STAR
RNA-seq
mapping
single-end
updated 1 hour ago by
GenoMax
152k • written 1 hour ago by
Manko47
▴ 10
0
votes
1
reply
74
views
Obtain Common SNPS for Mouse Genome
mouse
SNPs
updated 59 minutes ago by
GenoMax
152k • written 8 hours ago by
joe_genome
▴ 60
1
vote
2
replies
207
views
How do you clean GEO metadata before downstream analysis?
geo
updated 8 hours ago by
yura.grabovska
▴ 800 • written 2 days ago by
Alba
• 0
0
votes
1
reply
108
views
Seeking high-quality curated metabolic models with time-resolved flux data for sonification project
metabolism
sonification
networks
updated 13 hours ago by
Mensur Dlakic
★ 29k • written 16 hours ago by
omereilam1
• 0
0
votes
0
replies
74
views
Standard way to represent represent indel (insertion or deletion) alleles within a haplotype
haplotypes
indels
haploview
18 hours ago by
Mwangana
• 0
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
1
vote
1
reply
178
views
lovis4u Configuration
graph
lovis4u
genomics
updated 1 day ago by
GenoMax
152k • written 1 day ago by
NIkita
• 0
1
vote
1
reply
183
views
Tool:
Tool to clean GEO metadata
GEO
metadata
updated 8 hours ago by
yura.grabovska
▴ 800 • written 2 days ago by
Alba
• 0
0
votes
2
replies
453
views
WGBS Analysis with 1 control sample and 6 disease samples
one
WGBS
sample
updated 1 day ago by
ATpoint
88k • written 12 days ago by
Cassandra
• 0
0
votes
2
replies
480
views
How to extract gene list from GEO dataset in R
coding
beginner
question
r
updated 2 days ago by
Shohel
• 0 • written 12 days ago by
decorus
• 0
0
votes
6
replies
406
views
RNA seq strandedness (reverse-strand)
seq
reverse-stranded
strand
RNA
11 hours ago by
ZuelTech
• 0
0
votes
0
replies
146
views
TFs and enrichment analysis for TRAP sequencing
TRAP
2 days ago by
Genesis
• 0
0
votes
2
replies
226
views
Extract track data from "search by region" feature on ENCODE
Encode
4 hours ago by
AlienPumpkinPie
• 0
9
votes
8
replies
910
views
Weird p-value distribution on edgeR results
edgeR
pvalue-distribution
gene-expression
updated 2 days ago by
dariober
15k • written 11 days ago by
Guillermo
▴ 30
1
vote
3
replies
272
views
Draw GO tree for some GO ids with coloring
enrichment
GO
2 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
160
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
219
views
calculating coverage of gene in my metagenomes with samtools
samtools
depth
metagenome
coverage
updated 3 days ago by
Pierre Lindenbaum
166k • written 3 days ago by
lintonf
• 0
1
vote
1
reply
219
views
how to merge gbz files
vg
updated 3 days ago by
Jouni Sirén
▴ 680 • written 3 days ago by
lushjia
• 0
2
votes
1
reply
215
views
plotting read length distribution of Single End data
read_length_distribution
single_end_sequencing
WGS
3 days ago by
Meghan.T
▴ 10
4
votes
1
reply
265
views
Preranked GSEA permutation
GSEA
updated 3 days ago by
ATpoint
88k • written 4 days ago by
as823jk
• 0
1
vote
2
replies
336
views
why bwa-mem only return one read with pair-read end
sequencing
bwa-mem
updated 1 day ago by
rfran010
★ 1.6k • written 4 days ago by
QX
▴ 70
0
votes
1
reply
208
views
Identification problem of IDE-8 cell on culture with inverted microscope
IDE-8
updated 3 days ago by
rfran010
★ 1.6k • written 3 days ago by
Prashanta
• 0
0
votes
2
replies
332
views
Identifying RBP motifs overlapping exons
motifs
bedtools
RBP
updated 3 days ago by
GenoMax
152k • written 7 days ago by
RK
• 0
0
votes
0
replies
175
views
News:
Upcoming NGS Data Analysis Courses 2025
SingleCell
RNAseq
Epigenomics
Illumina
DNAseq
3 days ago by
ecSeq Bioinformatics
▴ 20
0
votes
1
reply
240
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
422
views
Identify SNP, Indel variants from a List of FASTA sequence
SNP
updated 4 days ago by
Mark
★ 1.7k • written 9 days ago by
Trinh
▴ 10
2
votes
15
replies
916
views
Which Reference Hg38 or T2T?? Both??
Host
Removal
4 days ago by
Jon
• 0
3
votes
2
replies
307
views
Can I transduce HEK293T with Cas9 lentivirus followed by transfection with sgRNAs?
lentivirus
Transduction
CRISPR
transfection
offtopic
updated 4 days ago by
jared.andrews07
★ 19k • written 4 days ago by
louisflower1999
• 0
3
votes
3
replies
377
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
335
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
430
views
Mapping to a template sequece
sequencing
4 days ago by
QX
▴ 70
0
votes
2
replies
371
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
363
views
Loss of strandedness in the Illumina Strandedness Total RNA protocol
Illumina
RNA-seq
reads
stranded
updated 5 days ago by
ATpoint
88k • written 5 days ago by
Anjan
▴ 840
0
votes
1
reply
341
views
Help using ShinyCell2 and Seurat v5 object.
shinycell
seurat
shiny
shinycell2
scRNA
updated 4 days ago by
antonioggsousa
3.4k • written 5 days ago by
Jamie
• 0
0
votes
0
replies
243
views
News:
Machine Learning for Multi-Omics Integration at the University of Barcelona– Dec 2025
Machine-Learning
Sulti-Omics
Depp-Learning
Data-Integration
BigData
5 days ago by
Physalia-courses
★ 2.6k
0
votes
0
replies
262
views
Compare alternative splicing patterns between human and mouse?
orthologs
rna-seq
splicing
alternative
5 days ago by
aboll
▴ 20
2
votes
6
replies
510
views
Trouble getting representatives from clustered_nr database
database
blast
3 days ago by
Adolfo
• 0
0
votes
0
replies
241
views
FindTransferAnchors (reference prediction) vs Manual Annotations
Seurat
6 days ago by
reddyornah
• 0
3
votes
4
replies
445
views
NCBI Datasets CLI Question
ncbi-datasets
6 days ago by
Bjorn
• 0
0
votes
0
replies
265
views
Incomplete assembly in HPRC dataset
pangenome
HPRC
reference
6 days ago by
ohell
• 0
4
votes
3
replies
425
views
Joint Calling for Large Germline WGS Cohort
NGS
RAM
cohort
Genomics
WGS
updated 6 days ago by
Jeremy Leipzig
23k • written 7 days ago by
j.k3096
▴ 20
2
votes
4
replies
448
views
how shoud the phred score be intepreted?
sequencing
updated 6 days ago by
GenoMax
152k • written 7 days ago by
QX
▴ 70
0
votes
3
replies
524
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
271
views
WGCNA analysis for Proteomics data
Proteomics
WGCNA
7 days ago by
Sumit Paliwal
▴ 40
3
votes
8
replies
6.7k
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
0
votes
1
reply
772
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
7 days ago by
ecSeq Bioinformatics
▴ 20
1
vote
0
replies
337
views
Can iHS and XP-EHH be applied to targeted sequencing data?
sequencing
targeted
ngs
ihs
9 days ago by
slzr_
▴ 10
2
votes
3
replies
548
views
PacBio amplicon reads partially aligned using minimap2 – library or analysis issue?
PacBio
minimap2
alignment
variants
pbmm2
6 days ago by
louisflower1999
• 0
121,552 results • Page
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Comment: lovis4u Confiduration
Answer: RNA-seq assigned alignments
Answer: Weird p-value distribution on edgeR results
Answer: Weird p-value distribution on edgeR results
Answer: Weird p-value distribution on edgeR results
How To Filter Mapped Reads With Samtools
Comment: How do you clean GEO metadata before downstream analysis?
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Recent Replies
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/…
Comment: WGBS Analysis with 1 control sample and 6 disease samples
by
ATpoint
88k
What is your analysis goal? Differential methylation? edgeR has a workflow (see its user guide) where 6 vs 1 would be supported. That is ob…
Comment: why bwa-mem only return one read with pair-read end
by
rfran010
★ 1.6k
Is this true for bwa-mem? I find generally this is not true, e.g. if I have 1 million paired reads with one alignment per read pair, I expe…
Comment: WGBS Analysis with 1 control sample and 6 disease samples
by
Shohel
• 0
For WGBS analysis with multiple samples you can solve it by one by one. Although you have only 7 samples. To analyze the WGBS file you can …
Comment: How to extract gene list from GEO dataset in R
by
Shohel
• 0
Hi I saw the GSE239903 dataset. It contains RNAseq data along with ATACseq data. To get the gene IDs you can follow the scRNA seq pipeline …
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