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121,548 results • Page
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0
votes
1
reply
91
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lovis4u Configuration
graph
lovis4u
genomics
updated 1 hour ago by
GenoMax
152k • written 17 hours ago by
NIkita
• 0
0
votes
0
replies
95
views
Tool:
Tool to clean GEO metadata
GEO
metadata
23 hours ago by
Alba
• 0
0
votes
0
replies
97
views
How do you clean GEO metadata before downstream analysis?
bioinformatics
geo
23 hours ago by
Alba
• 0
843
votes
170
replies
182k
views
112 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 10 weeks ago by
Biostar
3.6k • written 8.6 years ago by
Istvan Albert
102k
0
votes
2
replies
396
views
WGBS Analysis with 1 control sample and 6 disease samples
one
WGBS
sample
updated 5 hours ago by
ATpoint
88k • written 11 days ago by
Cassandra
• 0
0
votes
2
replies
417
views
How to extract gene list from GEO dataset in R
coding
beginner
question
r
updated 1 day ago by
Shohel
• 0 • written 11 days ago by
decorus
• 0
0
votes
5
replies
307
views
RNA seq strandedness (reverse-strand)
seq
reverse-stranded
strand
RNA
updated 1 day ago by
Shohel
• 0 • written 2 days ago by
ZuelTech
• 0
0
votes
0
replies
110
views
TFs and enrichment analysis for TRAP sequencing
TRAP
1 day ago by
Genesis
• 0
0
votes
1
reply
149
views
Extract track data from "search by region" feature on ENCODE
Encode
updated 1 day ago by
GenoMax
152k • written 1 day ago by
AlienPumpkinPie
• 0
6
votes
8
replies
848
views
Weird p-value distribution on edgeR results
edgeR
pvalue-distribution
gene-expression
updated 1 day ago by
dariober
15k • written 10 days ago by
Guillermo
▴ 30
1
vote
3
replies
213
views
Draw GO tree for some GO ids with coloring
enrichment
GO
1 day ago by
boczniak767
▴ 880
2
votes
4
replies
2.5k
views
Extract transcript fasta using gff
fasta
gff
updated 1 day ago by
cmdcolin
★ 4.2k • written 4.1 years ago by
boczniak767
▴ 880
0
votes
0
replies
126
views
Understanding MAG completeness and contig composition in metagenomic bins
data
shotgun
2 days ago by
shevch2009
▴ 20
1
vote
4
replies
1.1k
views
Problem with Mirdeep2 and Randfold output
mirdeep2
Randfold
updated 2 days ago by
Jasim
• 0 • written 15 months ago by
otieno43
▴ 40
0
votes
1
reply
180
views
calculating coverage of gene in my metagenomes with samtools
samtools
depth
metagenome
coverage
updated 2 days ago by
Pierre Lindenbaum
166k • written 2 days ago by
lintonf
• 0
1
vote
1
reply
180
views
how to merge gbz files
vg
updated 2 days ago by
Jouni Sirén
▴ 680 • written 2 days ago by
lushjia
• 0
2
votes
1
reply
180
views
plotting read length distribution of Single End data
read_length_distribution
single_end_sequencing
WGS
2 days ago by
Meghan.T
▴ 10
4
votes
1
reply
228
views
Preranked GSEA permutation
GSEA
updated 2 days ago by
ATpoint
88k • written 3 days ago by
as823jk
• 0
1
vote
2
replies
287
views
why bwa-mem only return one read with pair-read end
sequencing
bwa-mem
updated 18 hours ago by
rfran010
★ 1.6k • written 3 days ago by
QX
▴ 70
0
votes
1
reply
169
views
Identification problem of IDE-8 cell on culture with inverted microscope
IDE-8
updated 2 days ago by
rfran010
★ 1.6k • written 2 days ago by
Prashanta
• 0
0
votes
2
replies
297
views
Identifying RBP motifs overlapping exons
motifs
bedtools
RBP
updated 2 days ago by
GenoMax
152k • written 6 days ago by
RK
• 0
0
votes
0
replies
143
views
News:
Upcoming NGS Data Analysis Courses 2025
SingleCell
RNAseq
Epigenomics
Illumina
DNAseq
2 days ago by
ecSeq Bioinformatics
▴ 20
0
votes
1
reply
204
views
How to match clinical information with expression data in R
R
updated 3 days ago by
Arup Ghosh
3.3k • written 3 days ago by
py3296746920
• 0
3
votes
1
reply
391
views
Identify SNP, Indel variants from a List of FASTA sequence
SNP
updated 3 days ago by
Mark
★ 1.7k • written 8 days ago by
Trinh
▴ 10
2
votes
15
replies
851
views
Which Reference Hg38 or T2T?? Both??
Host
Removal
3 days ago by
Jon
• 0
3
votes
2
replies
264
views
Can I transduce HEK293T with Cas9 lentivirus followed by transfection with sgRNAs?
lentivirus
Transduction
CRISPR
transfection
offtopic
updated 3 days ago by
jared.andrews07
★ 19k • written 3 days ago by
louisflower1999
• 0
3
votes
3
replies
334
views
Mitochondrial annotation tool for algae
barcoding
annotation
updated 3 days ago by
Juke34
9.3k • written 4 days ago by
firefox91
• 0
1
vote
2
replies
283
views
Identifying gene outliers in a genome using composition analysis.
RSCU
composition
GC
outliers
updated 4 days ago by
GenoMax
152k • written 4 days ago by
Shakunthala Natarajan
• 0
1
vote
5
replies
375
views
Mapping to a template sequece
sequencing
3 days ago by
QX
▴ 70
0
votes
2
replies
334
views
quality control for 16s metagenome reads
quality
metagneome
control
16s
fastp
updated 4 days ago by
GenoMax
152k • written 6 days ago by
m90
▴ 30
0
votes
2
replies
327
views
Loss of strandedness in the Illumina Strandedness Total RNA protocol
Illumina
RNA-seq
reads
stranded
updated 4 days ago by
ATpoint
88k • written 4 days ago by
Anjan
▴ 840
0
votes
1
reply
305
views
Help using ShinyCell2 and Seurat v5 object.
shinycell
seurat
shiny
shinycell2
scRNA
updated 3 days ago by
antonioggsousa
3.4k • written 4 days ago by
Jamie
• 0
0
votes
0
replies
214
views
News:
Machine Learning for Multi-Omics Integration at the University of Barcelona– Dec 2025
Machine-Learning
Sulti-Omics
Depp-Learning
Data-Integration
BigData
4 days ago by
Physalia-courses
★ 2.6k
0
votes
0
replies
233
views
Compare alternative splicing patterns between human and mouse?
orthologs
rna-seq
splicing
alternative
4 days ago by
aboll
▴ 20
2
votes
6
replies
464
views
Trouble getting representatives from clustered_nr database
database
blast
2 days ago by
Adolfo
• 0
0
votes
0
replies
209
views
FindTransferAnchors (reference prediction) vs Manual Annotations
Seurat
4 days ago by
reddyornah
• 0
3
votes
4
replies
404
views
NCBI Datasets CLI Question
ncbi-datasets
5 days ago by
Bjorn
• 0
0
votes
0
replies
235
views
Incomplete assembly in HPRC dataset
pangenome
HPRC
reference
5 days ago by
ohell
• 0
4
votes
3
replies
389
views
Joint Calling for Large Germline WGS Cohort
NGS
RAM
cohort
Genomics
WGS
updated 5 days ago by
Jeremy Leipzig
23k • written 6 days ago by
j.k3096
▴ 20
2
votes
4
replies
415
views
how shoud the phred score be intepreted?
sequencing
updated 5 days ago by
GenoMax
152k • written 6 days ago by
QX
▴ 70
0
votes
3
replies
492
views
Inherited pipeline uses RNA-seq variant calls for WASP filtering—shouldn’t it be external SNPs?
WASP
updated 5 days ago by
i.sudbery
21k • written 8 days ago by
jonas.andersson
▴ 40
0
votes
0
replies
238
views
WGCNA analysis for Proteomics data
Proteomics
WGCNA
6 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 6 days ago by
zhang
• 0 • written 3.1 years ago by
firestar
★ 1.7k
0
votes
1
reply
738
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
6 days ago by
ecSeq Bioinformatics
▴ 20
1
vote
0
replies
308
views
Can iHS and XP-EHH be applied to targeted sequencing data?
sequencing
targeted
ngs
ihs
8 days ago by
slzr_
▴ 10
2
votes
3
replies
512
views
PacBio amplicon reads partially aligned using minimap2 – library or analysis issue?
PacBio
minimap2
alignment
variants
pbmm2
5 days ago by
louisflower1999
• 0
0
votes
0
replies
974
views
Job:
Biomedical Data Scientist / Systems Biologist / Omics Data Analyst / Bioinformatician / Computational Biologist (Tulane University, New Orleans, LA)
TUPulm
8 days ago by
yzhou40
• 0
0
votes
0
replies
357
views
Batch effect in codominant microsatellite data – how to correct
population-genetics
batch-effect
R
microsatellite
genotyping
8 days ago by
shervin
• 0
2
votes
3
replies
509
views
UCSC genome browser negative strand positions
Genomic
Data
Browser
UCSC
Visualization
Genome
updated 8 days ago by
Maximilian Haeussler
★ 1.8k • written 9 days ago by
ijarne
▴ 20
0
votes
1
reply
370
views
Error when computing bedtools bamtobed -bedpe
human
bedtools
libraries
illumina
bamtobed
updated 9 days ago by
ATpoint
88k • written 9 days ago by
María José
▴ 10
121,548 results • Page
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Answer: Can I transduce HEK293T with Cas9 lentivirus followed by transfection with sgRNA
bwa mem: Passing a variable to read group
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Recent Replies
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 …
Answer: RNA seq strandedness (reverse-strand)
by
Shohel
• 0
Hi, you can use hisat2 for alignment then Sam tools and then featurecount for coun matrix... Hisat2 code is hisat2 -x genome_index -1 read…
Comment: Extract track data from "search by region" feature on ENCODE
by
GenoMax
152k
Examples of the API don't show any region based examples. Not saying that is not possible but it would be an obvious example that would hav…
Comment: Draw GO tree for some GO ids with coloring
by
boczniak767
▴ 880
Thank you all for input. @jaredandrews07 - I have too many graphs to color them manually ;-). It is not the first time when I find answer …
Answer: Weird p-value distribution on edgeR results
by
dariober
15k
> On the other hand, it is possible to get an p-value histogram like you show if there is a massive batch effect and the batch effect is ba…
Answer: Draw GO tree for some GO ids with coloring
by
jared.andrews07
★ 19k
Frankly, I'd just get as close as possible and then re-color the significant terms in Illustrator or such. [genescape](https://github.co…
Answer: Extract transcript fasta using gff
by
cmdcolin
★ 4.2k
As long as this thread is revived, there is minigff now also https://github.com/lh3/minigff For gffread, the documentation for some reason…
Answer: Draw GO tree for some GO ids with coloring
by
txema.heredia
▴ 250
`clusterProfiler` has several tools to draw the results: https://yulab-smu.top/biomedical-knowledge-mining-book/enrichplot.html Even …
Comment: RNA seq strandedness (reverse-strand)
by
michael.ante
★ 4.0k
You can use [IGV][1] to look at your alignment using your reference and its gene-annotation. You'll see how your reads orient themselves in…
Comment: Identifying gene outliers in a genome using composition analysis.
by
Shakunthala Natarajan
• 0
Thank you. I will check them out.
Comment: RNA seq strandedness (reverse-strand)
by
GenoMax
152k
Use a standard tool like `featureCounts` as noted here --> https://www.biostars.org/p/9612088/#9612095
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