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116,606 results • Page
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News:
Master Meta-analysis with R (May 13-16) - Online!
MetaAnalysis
Statistics
R
just now by
carlopecoraro2
★ 2.5k
0
votes
0
replies
1
view
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
just now by
Emily
▴ 10
0
votes
0
replies
6
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
13 minutes ago by
rohitsatyam102
▴ 840
0
votes
2
replies
33
views
Sequence read length shorter than flow cell specification
illumina
NGS
sequencing
updated just now by
GenoMax
141k • written 1 hour ago by
M
• 0
795
votes
167
replies
141k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.7k • written 7.4 years ago by
Istvan Albert
100k
0
votes
0
replies
13
views
how to read graph_test output of monocle 3
monocle3
46 minutes ago by
synat.keam
▴ 100
0
votes
0
replies
19
views
Job:
CTO/founding engineer role at Voyant Bio
engineer
1 hour ago by
Assaf
• 0
0
votes
1
reply
346
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 1 hour ago by
ginellegrenier
• 0 • written 4 months ago by
Clayton
• 0
1
vote
1
reply
60
views
ScRNA data question
scRNA
Vlnplot
Samples
updated 2 hours ago by
bk11
★ 2.3k • written 2 hours ago by
starswillfade
▴ 10
1
vote
0
replies
41
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell
markers
3 hours ago by
Francesco
▴ 10
0
votes
0
replies
49
views
BLAST using both nucleotides and taxonomic local databases
blast
ncbi
taxid
taxonomy
5 hours ago by
Begonia_pavonina
▴ 150
2
votes
3
replies
101
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
updated 1 hour ago by
Pierre Lindenbaum
161k • written 6 hours ago by
QX
• 0
0
votes
1
reply
97
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
6 hours ago by
Assa Yeroslaviz
★ 1.8k
2
votes
1
reply
119
views
Finding orthologs between genome error
OMA
OMAbrowser
updated 7 hours ago by
Adrian Altenhoff
★ 1.1k • written 23 hours ago by
hemantcnaik
• 0
0
votes
0
replies
46
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
7 hours ago by
Aspire
▴ 300
2
votes
4
replies
186
views
Fetch table from clinvar database according to a list of rsid
clinvar
fetching
data
python
perl
7 hours ago by
ashaneev07
▴ 20
2
votes
3
replies
147
views
Figures are disappeared from html report of SnpEff
HTML
SnpEff
updated 5 hours ago by
Pierre Lindenbaum
161k • written 9 hours ago by
analyst
▴ 30
0
votes
1
reply
99
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment
gaps
updated 9 hours ago by
b.contreras.moreira
▴ 170 • written 10 hours ago by
Broccoli
• 0
0
votes
2
replies
125
views
Highest variable features in single cell data
cell
single
6 hours ago by
Kazo
• 0
0
votes
1
reply
130
views
Network Alignment
plugin
Cytoscape
CytoMCS
updated 12 hours ago by
Scooter
▴ 280 • written 1 day ago by
Akash D
▴ 40
2
votes
4
replies
2.3k
views
How could I generate a gi_taxid_nucl.dmp file similar to the one previously hosted by NCBI?
ncbi
metagenomics
centrifuge
gi_taxid_nucl.dmp
taxonomy
updated 13 hours ago by
ZhangYuanfeng
• 0 • written 2.4 years ago by
Frazier Baker
• 0
0
votes
1
reply
102
views
PCA plot
DESeq2
PCAplot
updated 2 hours ago by
jkim
▴ 170 • written 13 hours ago by
Aaliya
▴ 10
0
votes
0
replies
66
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
13 hours ago by
Ming Tommy Tang
★ 3.9k
0
votes
3
replies
260
views
Heatmap and rna-seq
RNA-Seq
Heatmap
and
updated 14 hours ago by
Kevin Blighe
87k • written 2 days ago by
qudrat.nii
▴ 10
0
votes
4
replies
2.6k
views
Lositan freezing when generating selection table
LOSITAN
updated 14 hours ago by
evawillms183
• 0 • written 8.3 years ago by
andrepleao
• 0
0
votes
0
replies
76
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
16 hours ago by
4fzcgueyp5
• 0
2
votes
3
replies
249
views
clustalo - align milions of short seq, memory issue
memory
clustalo
updated 2 days ago by
Mensur Dlakic
★ 27k • written 3 days ago by
emmanouil.a
▴ 120
0
votes
1
reply
129
views
Annovar using R package
Annovar
gnomAD
R
updated 18 hours ago by
Pierre Lindenbaum
161k • written 20 hours ago by
DKA
▴ 40
0
votes
2
replies
159
views
Creating Synthetic Sequences for a ML Model
DNA
ML
updated 18 hours ago by
Mensur Dlakic
★ 27k • written 22 hours ago by
biochugs
• 0
3
votes
8
replies
447
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 11 hours ago by
swbarnes2
14k • written 1 day ago by
Aaliya
▴ 10
1
vote
8
replies
723
views
Adding CB tag to bam file
samtools
bam
updated 8 hours ago by
Pierre Lindenbaum
161k • written 6 days ago by
Maria
• 0
1
vote
10
replies
873
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
21 hours ago by
DKA
▴ 40
0
votes
2
replies
762
views
AGeNT LocatIt
AGeNT
LocatIt
WES
UMI
duplicates
updated 1 day ago by
barslmn
★ 2.1k • written 2.8 years ago by
jhy
▴ 10
0
votes
5
replies
243
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 3 hours ago by
GenoMax
141k • written 1 day ago by
Bertalan_Takacs
▴ 90
0
votes
0
replies
102
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 21 hours ago by
Ram
43k • written 1 day ago by
glaciya2018
• 0
0
votes
0
replies
83
views
News:
8th Berlin Summer School in NGS Data Analysis - Apply Now
variantcalling
DNAseq
illumina
RNAseq
transcriptomics
1 day ago by
David Langenberger
11k
0
votes
0
replies
176
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
1 day ago by
pramach1
▴ 40
0
votes
14
replies
3.5k
views
6 follow
Tax4Fun2 - error
tax4fun
silva
blast
updated 1 day ago by
drstalinantony28
• 0 • written 2.2 years ago by
ymj
▴ 10
0
votes
1
reply
119
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 1 day ago by
Sofia
• 0 • written 1 day ago by
mawigoj318
• 0
0
votes
0
replies
103
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
1 day ago by
salias
• 0
4
votes
7
replies
371
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 8 hours ago by
dsull
★ 5.8k • written 1 day ago by
VITALA
• 0
0
votes
4
replies
223
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
8 hours ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
92
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 22 hours ago by
Ram
43k • written 1 day ago by
newuser2024
• 0
1
vote
2
replies
172
views
alignment result
RNA-seq
samtools
hisat2
11 hours ago by
ahmad.sajad4541
• 0
0
votes
0
replies
90
views
News:
hands-on introduction to generalized linear models (GLMs) using R
Generalized-Linear-Models
GLM
R
updated 21 hours ago by
Ram
43k • written 1 day ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
83
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
DoubletFinder
Seurat
modelHomotypic
updated 21 hours ago by
Ram
43k • written 1 day ago by
Jeyong
• 0
0
votes
2
replies
198
views
Wilcox test using data slot (log normalized count values) of scRNA-seq between two groups
scRNAseq
1 day ago by
mropri
▴ 150
2
votes
2
replies
185
views
HaplotypeCaller - only SNPs
HaplotypeCaller
GATK
updated 1 day ago by
analyst
▴ 30 • written 1 day ago by
lorena9132
• 0
0
votes
0
replies
96
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
1 day ago by
Kash
▴ 110
7
votes
2
replies
249
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 1 day ago by
geneontologyhelp
▴ 390 • written 3 days ago by
catherine.teyssier
• 0
116,606 results • Page
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Answer: How do I get the 3bp sequence on either side of a co-ordinate
What is the difference between HaplotypeCaller and UnifiedGenotyper?
What is the difference between HaplotypeCaller and UnifiedGenotyper?
RSeQC Output from infer_experiment.py - what does it mean?
ScRNAseq-How to correctly choose cell type marker genes
ScRNA data question
Comment: SRA to BAM
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Recent Replies
Comment: Sequence read length shorter than flow cell specification
by
GenoMax
141k
> the have sent data with different sequencing read lengths: 55bp pair ended and 80bp single ended If they sent data that is not what you…
Comment: How to know synonymous and non-synonymous SNPs from transcriptome sequencing
by
rohitsatyam102
▴ 840
I have some off-the-chart dN/dS values for few genes (>20) when using your script on VCF obtained from a 20K plasmodium genomes (pf7K). | …
Answer: Sequence read length shorter than flow cell specification
by
ATpoint
82k
It is the amount of reagent in the kit that determines read length. Sometimes index cycle reagents are allocated to R1/R2 or they used anot…
Comment: Why gatk VariantAnnotator required bam and coverage files
by
Pierre Lindenbaum
161k
you don't need the bam file https://gatk.broadinstitute.org/hc/en-us/articles/13832654601755-VariantAnnotator : VariantAnnotator …
Comment: GAPIT p-value significance threshold
by
ginellegrenier
• 0
Hi, I was wondering if you have found a solution to this? Thanks!
Comment: PCA plot
by
jkim
▴ 170
cross posted in bioconductor. [https://support.bioconductor.org/p/9157968/][1] [1]: https://support.bioconductor.org/p/9157968/
Comment: ScRNA data question
by
bk11
★ 2.3k
Which normalization method did you use for your data? I am guessing you had used SCTransform normalization for your data. Can you plot usin…
Comment: How to make a TSS enrichment plot in ATAC-seq analysis?
by
sp
• 0
Hi Dan, I was wondering if you found out how to make the same graph with NFR and NBR regions with different curves. I was able to recreate…
Comment: Why gatk VariantAnnotator required bam and coverage files
by
QX
• 0
I think the coverage could also computed from bam file itself, but let say I do not include the coverage, do you have any idea why it needs…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas
by
GenoMax
141k
I am moving my answer to a comment. At this point you should email NCBI help desk and ask them this question. If you get an answer then ple…
Comment: Figures are disappeared from html report of SnpEff
by
Pierre Lindenbaum
161k
the javascript in your html is deprecated or your firefox is just tool old.
Comment: Why gatk VariantAnnotator required bam and coverage files
by
Pierre Lindenbaum
161k
> I would like to ask why they may require the bam file for this function? hum.. if you want to add the coverage, where do you think gatk …
Comment: Figures are disappeared from html report of SnpEff
by
analyst
▴ 30
By following above approach I got this ![enter image description here][1] [1]: /media/images/b47490eb-d4c4-4f39-a7b2-f5b7b6b8
Comment: Highest variable features in single cell data
by
Kazo
• 0
I apologize for the confusion. What I meant to say is that, for example, the Trbv17 gene appears among the variable genes. However, when I …
Answer: why renaming Idents in Seurat object doesn't work?
by
Assa Yeroslaviz
★ 1.8k
I manage to find a workwround, but I don't understand what I did wrong here. my solution was to extract the cluster column as vector and…
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