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116,960 results • Page
1 of 2340
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1
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1
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112
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
22 minutes ago by
ramiro.barrantes
• 0
1
vote
1
reply
69
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
updated 41 minutes ago by
marco.barr
▴ 120 • written 5 hours ago by
diqixiaoyaoer
▴ 10
2
votes
6
replies
1.8k
views
How can you *consistently* download BioProject IDs from NCBI's BioSample database using Entrez Direct?
XML
ncbi
entrez-direct
updated 10 minutes ago by
Ram
43k • written 3.9 years ago by
millere
• 0
0
votes
2
replies
138
views
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
rstudio
DEG
limma
updated 1 hour ago by
swbarnes2
14k • written 10 hours ago by
egascon
• 0
0
votes
0
replies
18
views
What's next after GATK variant calling pipeline?
GATK
pipeline
figures
DNA-seq
1 hour ago by
mgranada3
▴ 30
797
votes
167
replies
143k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.8k • written 7.4 years ago by
Istvan Albert
100k
0
votes
0
replies
20
views
Add line under stat test
stats
R
1 hour ago by
Ghada
• 0
1
vote
5
replies
729
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
written 6 months ago by
Daniel
▴ 30
0
votes
0
replies
35
views
DOCK6 installation on MacOS M1
installation
troubleshooting
DOCK6
updated 3 hours ago by
GenoMax
142k • written 3 hours ago by
Rodolfo Adrián
• 0
1
vote
3
replies
110
views
Genotyping sites with N in reference genome
GATK
UnifiedGenotyper
updated 3 hours ago by
Zhenyu Zhang
★ 1.2k • written 4 hours ago by
shpak.max
▴ 50
0
votes
1
reply
76
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
updated 4 hours ago by
yura.grabovska
▴ 70 • written 4 hours ago by
ev97
▴ 20
0
votes
2
replies
86
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
meta
how-to
ncbi
forum
3 hours ago by
hophuquy0944
• 0
0
votes
2
replies
93
views
Sequencing Depth (Read Depth) Calculations
depth
updated 5 hours ago by
GenoMax
142k • written 5 hours ago by
jiahangkui1234
• 0
0
votes
1
reply
72
views
Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
annotation
vcf
vep
zygosity
deepvariant
4 hours ago by
asalimih
▴ 60
0
votes
0
replies
50
views
Is it okay to assemble my 12 metatranscriptome samples with Trinity separately?
trinity
metatranscriptome
5 hours ago by
jway
• 0
2
votes
2
replies
108
views
Cannot install bwa-mem2 via conda
conda
mamba
python
code
updated 5 hours ago by
Istvan Albert
100k • written 6 hours ago by
jsmith120f
• 0
2
votes
2
replies
135
views
genome finishing
finishing
genome
updated 6 hours ago by
nd48
▴ 20 • written 10 hours ago by
trezini
• 0
1
vote
5
replies
153
views
Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
circos
atacseq
updated 6 hours ago by
Pierre Lindenbaum
161k • written 7 hours ago by
biology_inform
▴ 50
1
vote
4
replies
194
views
Add stats to boxplot in R
stats
R
3 hours ago by
Ghada
• 0
0
votes
0
replies
60
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
updated 6 hours ago by
ATpoint
82k • written 7 hours ago by
yura.grabovska
▴ 70
0
votes
0
replies
52
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base
calling
nanopore
simplex
dorado
duplex
7 hours ago by
Lélé
▴ 10
0
votes
3
replies
97
views
Tool:
Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Minutes
Decimal
Degrees
python
Degree
offtopic
updated 7 hours ago by
Joe
21k • written 7 hours ago by
kuttibiotech2009
▴ 30
0
votes
3
replies
137
views
calculating genomic coverage/ base overlap in R
bioinoformatics
genomics
updated 3 hours ago by
marco.barr
▴ 120 • written 9 hours ago by
Sayantani
• 0
0
votes
2
replies
82
views
Annotating file using bcftools
annotation
plink
bcftools
updated 8 hours ago by
Pierre Lindenbaum
161k • written 10 hours ago by
kl
▴ 10
0
votes
8
replies
251
views
Duplicated reads (IDs) from nanopore sequencing
bam
nanopore
sequencing
updated 6 hours ago by
GenoMax
142k • written 14 hours ago by
njornet
▴ 20
0
votes
3
replies
107
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
10 hours ago by
Esraa
• 0
1
vote
1
reply
99
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm
ChIP-seq
consensus
peaks
updated 11 hours ago by
ATpoint
82k • written 12 hours ago by
Alexandra
• 0
1
vote
1
reply
179
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
updated 12 hours ago by
dariober
14k • written 1 day ago by
Holly
▴ 10
1
vote
3
replies
141
views
Filtering VCF files based on VAF giving incorrect results
bcftools
GATK
Bioinformatics
picard
VCF
updated 59 minutes ago by
Pierre Lindenbaum
161k • written 16 hours ago by
Arton
• 0
0
votes
0
replies
60
views
ReactomeGSA
ReactomeGSA
13 hours ago by
Shaimaa Gamal
▴ 10
0
votes
0
replies
55
views
News:
New course: Manipulation of NGS Data for Genomic and Population Genetics Analyses
KeepLearning
TScourses
13 hours ago by
Transmitting Science communication
▴ 70
0
votes
1
reply
98
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 9 hours ago by
GenoMax
142k • written 15 hours ago by
chrisk
• 0
0
votes
1
reply
103
views
perseus software (version 1.5.5)
preseus
mass
spectrometry
data
updated 7 hours ago by
Joe
21k • written 17 hours ago by
iqra
• 0
0
votes
0
replies
74
views
Why the shape of RCS is contradictory to the p value for nonlinearity.
RCS
ggplot2
ggplot
R
updated 18 hours ago by
GenoMax
142k • written 19 hours ago by
Dude
• 0
0
votes
0
replies
68
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
19 hours ago by
brunofelicianodeomena
• 0
1
vote
2
replies
162
views
Alphafold 3 pLDDT coloring scheme in chimerax?
ChimeraX
Alphaphold
Alphaphold3
updated 14 hours ago by
colindaven
6.4k • written 21 hours ago by
mbrav005
• 0
0
votes
1
reply
121
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
17 hours ago by
sansan_96
▴ 90
1
vote
2
replies
145
views
Doubt about the process of annotation, detection, identification and classification of transposable elements
annotation
TransposableElements
1 hour ago by
MarcosCosta
• 0
2
votes
2
replies
175
views
Genome Visualization Tools
bacterial
genome
updated 1 day ago by
GenoMax
142k • written 1 day ago by
dlera.lozano
▴ 10
2
votes
3
replies
184
views
RSeQC : infer_experiment.py Error: Could not retrieve index file
RSeQC
RNA-Seq
updated 1 day ago by
Ram
43k • written 1 day ago by
Prawesh
• 0
0
votes
3
replies
236
views
Using ggplotly in R
ggplot
ggplotly
updated 5 hours ago by
jared.andrews07
★ 16k • written 1 day ago by
jen
▴ 10
0
votes
1
reply
141
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
updated 1 day ago by
GenoMax
142k • written 1 day ago by
bioinfo
▴ 150
0
votes
3
replies
229
views
RNAseq RNA content
mRNA
Linux
rRNA
RNA-seq
RNA
updated 1 day ago by
noodle
▴ 580 • written 1 day ago by
doramora
▴ 10
0
votes
1
reply
130
views
Post-imputation QC for input into GWAS analyses
gwas
prs
updated 1 day ago by
LauferVA
4.2k • written 1 day ago by
graeme.thorn
▴ 100
0
votes
2
replies
161
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
13 hours ago by
melissa.joubert
• 0
4
votes
1
reply
185
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
1 day ago by
J.
▴ 40
0
votes
0
replies
98
views
Is there a real ground truth for CNV data?
CNV
1 day ago by
jennyp0706
• 0
0
votes
3
replies
198
views
Biomart issue, why so few 3'utrs?
utr
biomart
updated 1 day ago by
GenoMax
142k • written 1 day ago by
RNAseqer
▴ 270
1
vote
1
reply
132
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 1 day ago by
Ram
43k • written 1 day ago by
kilcdincer
▴ 10
4
votes
4
replies
2.9k
views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
updated 1 day ago by
Anitha
• 0 • written 5.1 years ago by
stephaniem
• 0
116,960 results • Page
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Answer: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: Calculate allelic frequency from VEP output vcf file
Answer: How can you *consistently* download BioProject IDs from NCBI's BioSample databas
Answer: Cluster sub-set analysis using Seurat
Answer: Cannot install bwa-mem2 via conda
Answer: Cluster sub-set analysis using Seurat
Answer: featureCounts output summary assigned value higher than uniquely mapped reads fr
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Recent Replies
Answer: Calculate allelic frequency from VEP output vcf file
by
ramiro.barrantes
• 0
Found the answer here!! https://github.com/Illumina/strelka/blob/master/docs/userGuide/README.md#somatic Although this leads to a str…
Comment: Using VEP annotation output as the input for a second VEP annotation
by
Ram
43k
That's not a valid reason to delete the post. If that information was sensitive, posting it here was a mistake in the first place. I don't …
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
by
marco.barr
▴ 120
Hi, regardless of how you generated the data whether with DESeq2 or other pipeline, your differential expression matrix can be used as inpu…
Comment: Filtering VCF files based on VAF giving incorrect results
by
Pierre Lindenbaum
161k
> Do you think my commands were correct? I'm not familiar enough with this bcftools syntax. but what if there is no AD, what if both…
Answer: How can you *consistently* download BioProject IDs from NCBI's BioSample databas
by
Ash
▴ 10
I know this was asked several years ago, but finding this post helped me solve my own problem and in the process I solved this one too. …
Answer: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
swbarnes2
14k
Would Parkinson's be expected to have an effect on blood cells? Neurons, sure, but blood cells?
Comment: Doubt about the process of annotation, detection, identification and classificat
by
MarcosCosta
• 0
Thank you very much, you've helped me a lot. Could you suggest a book or article that offers a complete explanation of these processes?
Comment: Filtering VCF files based on VAF giving incorrect results
by
Arton
• 0
Thank you. I can't try a completely new tool but I will keep your command for future use. Do you think my commands were correct? For exampl…
Comment: Add stats to boxplot in R
by
Ghada
• 0
Thanks. Thats work
Comment: Genotyping sites with N in reference genome
by
Zhenyu Zhang
★ 1.2k
Whether N -> A/T/G/C represents a variant is heavily dependent on the tool itself, and I know most tools don't. Since you don't see it in y…
Comment: calculating genomic coverage/ base overlap in R
by
marco.barr
▴ 120
The code seems correct at first glance... How did you generate the data in the Excel file? Have you checked the exon annotations? You could…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Did you remeber to unzip/untar the `nt` preformatted files that you downloaded?
Comment: Genotyping sites with N in reference genome
by
shpak.max
▴ 50
Just to clarify, I have set additional sites in the reference genome to 'N', which means (based on your statement) that these will not be g…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
Pierre Lindenbaum
161k
see https://www.biostars.org/p/9496674/ <!-- when i runed blastn(version 2.15) and nt database(latest version). I used aspera to download…
Answer: Genotyping sites with N in reference genome
by
Pierre Lindenbaum
161k
> Does UnifiedGenotyper skip/ignore sites where the reference genotype is N yes. The variant is in YOUR data, not in the reference where '…
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