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121,099 results • Page
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About FastP Tool
Raw
Quality_control
Preprocessing
alignment
reads
updated 1 hour ago by
GenoMax
151k • written 4 hours ago by
AIMAR
• 0
0
votes
2
replies
142
views
Transcript identification and quantification
splitseq
transcript
scRNA
updated 2 hours ago by
ATpoint
88k • written 19 hours ago by
anton.avramov
• 0
836
votes
170
replies
175k
views
112 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 5 days ago by
Biostar
3.5k • written 8.4 years ago by
Istvan Albert
102k
0
votes
1
reply
84
views
Treatment of nanoparticles after buying before the experiment
fermentation
treatment
Nanoparticles
dark
updated 8 hours ago by
ATpoint
88k • written 12 hours ago by
Nick
• 0
1
vote
0
replies
72
views
Tool:
Accessible color palettes for charts and dataviz
dataviz
19 hours ago by
Pierre
▴ 10
2
votes
3
replies
154
views
Warning in bcftools when subsetting a VCF by variant ID
bcftools
VCF
Beagle5.5
updated 19 hours ago by
Pierre Lindenbaum
166k • written 21 hours ago by
Mwangana
• 0
1
vote
2
replies
144
views
Lucidea Array Spotter - Question about machinery
sequencing
Microarray
updated 22 hours ago by
GenoMax
151k • written 1 day ago by
Taylor
• 0
2
votes
2
replies
145
views
Deduplication rate of shotgun metagenomes using fastqc
metagenome
fastqc
shotgun
deduplication
updated 1 day ago by
GenoMax
151k • written 1 day ago by
vikasmh111
• 0
0
votes
3
replies
200
views
Differeces between Seurat::RunPCA and scater::runPCA affect downstream analyses
slingshot
PCA
Seurat
scater
single-cell
updated 1 day ago by
Bastien Hervé
6.2k • written 1 day ago by
txema.heredia
▴ 210
1
vote
1
reply
128
views
What is the difference between JASPAR IDs MA0668.3 and MA1993.2 for Neurod2?
motifs
atac-seq
factor
jaspar
transcription
updated 1 day ago by
GenoMax
151k • written 1 day ago by
Ambuj
• 0
0
votes
3
replies
201
views
How can I find KO IDs for ORF sequences in a large FASTA file?
KEGG
ORF
updated 1 day ago by
Ram
45k • written 1 day ago by
Nikesh
• 0
0
votes
0
replies
99
views
Single MAG Recruitment to multiple metaT Samples
metagenomics
rna-seq
transcriptomics
1 day ago by
zjhennin
• 0
0
votes
1
reply
938
views
Normalization - Tissue specificity analysis
gtex
updated 1 day ago by
Pallavi
• 0 • written 4.1 years ago by
Filago
▴ 100
2
votes
4
replies
2.9k
views
Transcript Specific Expression Data
rna-seq
updated 1 day ago by
Pallavi
• 0 • written 12.5 years ago by
disco
▴ 30
9
votes
6
replies
7.8k
views
6 follow
Database To Look For Tissue-Specific Transcript Expression Of The Same Gene.
transcript
updated 1 day ago by
Pallavi
• 0 • written 12.2 years ago by
michealsmith
▴ 800
6
votes
5
replies
1.9k
views
Tool:
Bioinformatics Docker Images Project (https://pegi3s.github.io/dockerfiles/)
containers
docker
updated 1 day ago by
GenoMax
151k • written 6.2 years ago by
pegi3sdocker
▴ 10
1
vote
0
replies
147
views
Job:
Looking for a mentor
health
mentor
informatics
updated 1 day ago by
GenoMax
151k • written 2 days ago by
yoav.lama
▴ 10
0
votes
0
replies
142
views
Job:
Postdoc fellow - genetics, proteomics, single cell and bioinformatics, Indiana University, Indianapolis, USA
proteomics
genetics
cell
single
bioinformatics
updated 2 days ago by
GenoMax
151k • written 2 days ago by
Jingwen
• 0
0
votes
0
replies
121
views
Strand bias and placement bias in variant calls
Variant
filter
updated 2 days ago by
Pierre Lindenbaum
166k • written 2 days ago by
Carolyn
• 0
0
votes
0
replies
128
views
STARsolo for multiome GEX: trimming (--clip5pNbases) & whitelist handling
STARSolo
multiome
whitelist
clip5pNbases
2 days ago by
IrK
▴ 100
1
vote
8
replies
344
views
Featurecounts: Unexpected number of features
featurecounts
1 day ago by
JourneyToAbyss
▴ 240
4
votes
13
replies
10k
views
7 follow
GVSA: problem with gene identifier
gvsa
RNA-Seq
gsea
updated 2 days ago by
Saravana
• 0 • written 8.0 years ago by
cmgraef
▴ 10
0
votes
0
replies
127
views
News:
Workshop: Virtual Variant Detection, May 20-22
VariantDetection
Workshop
UConn
2 days ago by
zsc25001
• 0
0
votes
0
replies
135
views
Plink vcf file output reporting
vcf
2 days ago by
1769mkc
★ 1.3k
1
vote
3
replies
264
views
Best way to combine biological replicate peaks?
ATAC-seq
updated 2 days ago by
jared.andrews07
★ 18k • written 3 days ago by
SpartanII
• 0
1
vote
5
replies
289
views
Filtering HMMSCAN Domtblout Output when using Metagenomic Sequence as Input
hmmscan
sequences
domtblout
metagenomic
updated 2 days ago by
Mensur Dlakic
★ 29k • written 2 days ago by
Jane123
• 0
0
votes
1
reply
196
views
I have doubts regarding conducting meta-analysis of differentially expressed genes
meta-analysis
Differential-Gene-Expression
updated 2 days ago by
LChart
4.9k • written 3 days ago by
Rohan
• 0
0
votes
3
replies
237
views
Create local Blast database alias with blastdb_aliastool fails
blast
updated 1 day ago by
GenoMax
151k • written 3 days ago by
etienne
• 0
2
votes
2
replies
274
views
Why is this interaction result not significant in DESeq2
DEG
DE
interaction
DESeq2
RNA-seq
updated 2 days ago by
yura.grabovska
▴ 760 • written 4 days ago by
Guillermo
▴ 10
0
votes
0
replies
137
views
Combining scRNA-seq datasets that have been processed differently
immunology
Seurat
3 days ago by
S
• 0
6
votes
8
replies
12k
views
7 follow
WGCNA package in R: dendogram plot error
wgcna
R
updated 3 days ago by
GenoMax
151k • written 8.3 years ago by
zyr123
▴ 40
1
vote
1
reply
191
views
Problem with galaxy's Maxquant
Proteomics
Maxquant
Galaxy
updated 3 days ago by
GenoMax
151k • written 3 days ago by
Chris K
▴ 10
0
votes
0
replies
138
views
Workflow for DE after high-resolution CibersortX deconvolution
CibersortX
Deconvolution
3 days ago by
Aspire
▴ 380
0
votes
0
replies
141
views
Is there any way to treat antibody titers as continuous data for microbiome analysis?
antibody-titers
immunology
microbiome
3 days ago by
nmarin
• 0
0
votes
0
replies
762
views
How to analyze transcriptional trends over time from multiple RNA-seq datasets with similar but not identical conditions?
pathway-analysis
rnaseq
differential-expression
meta-analysis
time-series
3 days ago by
enee
▴ 20
0
votes
0
replies
135
views
News:
9th Berlin Summer School in NGS Data Analysis 2025 (June 30 - July 4, 2025) -- SUMMER IN BERLIN --
Workshop
RNA-Seq
transcriptomics
VariantCalling
DNA-Seq
3 days ago by
ecSeq Bioinformatics
▴ 20
53
votes
11
replies
49k
views
When and why is bwa aln better then bwa mem?
aln
comparison
bwa
mem
3 days ago by
dariober
15k
0
votes
1
reply
177
views
How to deal polyploid and aneuploid sugarcane genome R570 for variant calling
aneuploid
updated 1 day ago by
dthorbur
★ 2.9k • written 3 days ago by
analyst
▴ 60
0
votes
2
replies
217
views
False positives annotation of Augustus?
Augustus
training
updated 3 days ago by
lieven.sterck
15k • written 3 days ago by
Joseph
• 0
1
vote
2
replies
311
views
Mapping SNPs to genes
biomart
SNP
ensembl
r
gene
3 days ago by
Nigussie
• 0
0
votes
2
replies
221
views
Rockhopper Reference Genome Error
Rockhopper
3 days ago by
ATS
• 0
0
votes
0
replies
150
views
What can cause Faststructure to produce really high K clusters as optimal (e.g. 12 - 14)
SNP
vcf
population
3 days ago by
Drew
▴ 10
0
votes
7
replies
1.2k
views
Trouble finding datasets
GEO
SRA
updated 3 days ago by
ehaag
▴ 20 • written 18 months ago by
SHXVRR
▴ 20
4
votes
2
replies
1.0k
views
Imputation server failing to see samples in VCF files
imputation
VCF
updated 3 days ago by
Andresa Raquel Capodifoglio
• 0 • written 19 months ago by
Ben
▴ 10
0
votes
3
replies
260
views
Read Mapping of Reads to Reference Genome Shows Extreme Bias
mapping
read
bwa-mem
coverage
updated 3 days ago by
Michael
55k • written 3 days ago by
Lawrence
• 0
0
votes
0
replies
161
views
News:
Introduction to Python for Biologists (IPYB01)
Python
updated 3 days ago by
GenoMax
151k • written 3 days ago by
oliverhooker
▴ 110
0
votes
0
replies
161
views
News:
Machine Learning using Python (MLUP01)
Python
updated 3 days ago by
GenoMax
151k • written 3 days ago by
oliverhooker
▴ 110
2
votes
2
replies
249
views
Interpreting a vcf file
variant
vcf
updated 1 day ago by
cmdcolin
★ 4.2k • written 4 days ago by
ramiro.barrantes
▴ 20
3
votes
0
replies
194
views
Herald:
The Biostar Herald for Tuesday, April 29, 2025
herald
4 days ago by
Biostar
3.5k
5
votes
2
replies
355
views
Best choices for DGE and pathway enrichment analysis in single cell data using pseudobulk?
DEG
GSEA
single-cell
pseudobulk
1 day ago by
txema.heredia
▴ 210
121,099 results • Page
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Recent Votes
Accessible color palettes for charts and dataviz
Answer: Warning in bcftools when subsetting a VCF by variant ID
Answer: Warning in bcftools when subsetting a VCF by variant ID
Answer: Deduplication rate of shotgun metagenomes using fastqc
Remove short sequences with length < 50% from a multi-fasta file
Answer: Remove short sequences with length < 50% from a multi-fasta file
Answer: Remove short sequences with length < 50% from a multi-fasta file
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Popular Question
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dalibenam64
• 0
Popular Question
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DareDevil
★ 4.4k
Scholar
to
Pierre Lindenbaum
166k
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odi
▴ 10
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Recent Replies
Answer: About FastP Tool
by
GenoMax
151k
> After using the gatk CollectSummaryAlignment command to have an idea about my aligne reads, it shows that the minimum length is about 19 …
Answer: Transcript identification and quantification
by
dsull
★ 7.4k
I regularly work on combinatorial barcoding data. If you’re open to a pseudoalignment approach, kallisto (via `kb-python`) can process P…
Answer: Transcript identification and quantification
by
ATpoint
88k
> Are there any better ways to do what ... Parse offers a pipeline for that which is automated (and a bit of a pain but do-able). Contact …
Comment: Treatment of nanoparticles after buying before the experiment
by
ATpoint
88k
This is off-topic here, and experimental design in general should be discussed with your PI and peers to eactly gget "more experienced peop…
Comment: Genomic Data Portal (GDC) download a given a link file
by
Zhenyu Zhang
★ 1.3k
download using gdc-client?
Comment: Warning in bcftools when subsetting a VCF by variant ID
by
Pierre Lindenbaum
166k
the message comes from the first bcftools. verify by running gunzip -c instead of bcftools ``` gunzip -c reheader_6_chrfixed_filtered_im…
Comment: Warning in bcftools when subsetting a VCF by variant ID
by
Mwangana
• 0
@Pierre Lindenbaum, this works perfectly well as it prints to the screen correctly but the error returns when I redirect it to a file: …
Answer: Warning in bcftools when subsetting a VCF by variant ID
by
Pierre Lindenbaum
166k
``` bcftools view reheader_6_chrfixed_filtered_imputed.vcf.gz |\ awk '/^#CHROM/ {printf("##INFO=<ID=END,Number=1,Type=Integer,Descript…
Comment: Differeces between Seurat::RunPCA and scater::runPCA affect downstream analyses
by
Bastien Hervé
6.2k
> Are scater::runPCA's underlying assumptions/method incompatible with SCT transformation? Potentially. Could you try doing a dummy test w…
Comment: What is the difference between JASPAR IDs MA0668.3 and MA1993.2 for Neurod2?
by
GenoMax
151k
While we wait for answers in this specific case, it may be best to post your question at JASPAR's google group site: https://groups.google.…
Comment: How can I find KO IDs for ORF sequences in a large FASTA file?
by
Mensur Dlakic
★ 29k
I don't think anyone can help you when the only feedback you provide is "there are some errors occurring." If I told you that I tried to bu…
Comment: How can I find KO IDs for ORF sequences in a large FASTA file?
by
Nikesh
• 0
Hi t tried to work with this, but there are some errors occurring, Do you have code or any source material to work on this ? @mensur
Comment: Differeces between Seurat::RunPCA and scater::runPCA affect downstream analyses
by
txema.heredia
▴ 210
Thanks for your input. Yes, the cell types are closely related. Both cell types have already been identified in multiple single cell paper…
Comment: How to deal polyploid and aneuploid sugarcane genome R570 for variant calling
by
dthorbur
★ 2.9k
Is there any way to estimate ploidy from the supplier, or from the ancestors that established the hybrids? I would suggest making an educ…
Comment: Lucidea Array Spotter - Question about machinery
by
Taylor
• 0
Thank you so much!
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