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116,603 results • Page
1 of 2333
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0
votes
0
replies
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views
Sequence read length shorter than flow cell specification
illumina
NGS
sequencing
3 minutes ago by
M
• 0
0
votes
1
reply
342
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 42 minutes ago by
ginellegrenier
• 0 • written 4 months ago by
Clayton
• 0
1
vote
1
reply
41
views
ScRNA data question
scRNA
Vlnplot
Samples
updated 1 hour ago by
bk11
★ 2.3k • written 1 hour ago by
starswillfade
▴ 10
1
vote
0
replies
31
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell
markers
2 hours ago by
Francesco
▴ 10
0
votes
0
replies
37
views
Calling SE and TE using ROSE
Calling
SE
3 hours ago by
Manhezz
• 0
0
votes
0
replies
46
views
BLAST using both nucleotides and taxonomic local databases
blast
ncbi
taxid
taxonomy
4 hours ago by
Begonia_pavonina
▴ 150
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
2
votes
3
replies
89
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
updated 10 minutes ago by
Pierre Lindenbaum
161k • written 5 hours ago by
QX
• 0
0
votes
1
reply
90
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
5 hours ago by
Assa Yeroslaviz
★ 1.8k
2
votes
1
reply
114
views
Finding orthologs between genome error
OMA
OMAbrowser
updated 6 hours ago by
Adrian Altenhoff
★ 1.1k • written 22 hours ago by
hemantcnaik
• 0
0
votes
0
replies
44
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
6 hours ago by
Aspire
▴ 300
2
votes
4
replies
179
views
Fetch table from clinvar database according to a list of rsid
clinvar
fetching
data
python
perl
6 hours ago by
ashaneev07
▴ 20
2
votes
3
replies
139
views
Figures are disappeared from html report of SnpEff
HTML
SnpEff
updated 4 hours ago by
Pierre Lindenbaum
161k • written 8 hours ago by
analyst
▴ 30
0
votes
1
reply
95
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment
gaps
updated 8 hours ago by
b.contreras.moreira
▴ 170 • written 9 hours ago by
Broccoli
• 0
0
votes
2
replies
119
views
Highest variable features in single cell data
cell
single
5 hours ago by
Kazo
• 0
0
votes
1
reply
128
views
Network Alignment
plugin
Cytoscape
CytoMCS
updated 11 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 11 hours ago by
ZhangYuanfeng
• 0 • written 2.4 years ago by
Frazier Baker
• 0
0
votes
1
reply
88
views
PCA plot
DESeq2
PCAplot
updated 1 hour ago by
jkim
▴ 170 • written 12 hours ago by
Aaliya
▴ 10
0
votes
0
replies
63
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
12 hours ago by
Ming Tommy Tang
★ 3.9k
0
votes
3
replies
256
views
Heatmap and rna-seq
RNA-Seq
Heatmap
and
updated 13 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 13 hours ago by
evawillms183
• 0 • written 8.3 years ago by
andrepleao
• 0
0
votes
0
replies
74
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
14 hours ago by
4fzcgueyp5
• 0
2
votes
3
replies
246
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
128
views
Annovar using R package
Annovar
gnomAD
R
updated 17 hours ago by
Pierre Lindenbaum
161k • written 19 hours ago by
DKA
▴ 40
0
votes
2
replies
155
views
Creating Synthetic Sequences for a ML Model
DNA
ML
updated 17 hours ago by
Mensur Dlakic
★ 27k • written 21 hours ago by
biochugs
• 0
3
votes
8
replies
440
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 10 hours ago by
swbarnes2
14k • written 1 day ago by
Aaliya
▴ 10
1
vote
8
replies
720
views
Adding CB tag to bam file
samtools
bam
updated 7 hours ago by
Pierre Lindenbaum
161k • written 6 days ago by
Maria
• 0
1
vote
10
replies
869
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
20 hours ago by
DKA
▴ 40
0
votes
2
replies
761
views
AGeNT LocatIt
AGeNT
LocatIt
WES
UMI
duplicates
updated 23 hours ago by
barslmn
★ 2.1k • written 2.8 years ago by
jhy
▴ 10
0
votes
5
replies
233
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 2 hours ago by
GenoMax
141k • written 1 day ago by
Bertalan_Takacs
▴ 90
0
votes
0
replies
99
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 20 hours ago by
Ram
43k • written 1 day ago by
glaciya2018
• 0
0
votes
0
replies
82
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
173
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
116
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
102
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
1 day ago by
salias
• 0
4
votes
7
replies
363
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 7 hours ago by
dsull
★ 5.8k • written 1 day ago by
VITALA
• 0
0
votes
4
replies
220
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
7 hours ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
89
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 20 hours ago by
Ram
43k • written 1 day ago by
newuser2024
• 0
1
vote
2
replies
167
views
alignment result
RNA-seq
samtools
hisat2
9 hours ago by
ahmad.sajad4541
• 0
0
votes
0
replies
88
views
News:
hands-on introduction to generalized linear models (GLMs) using R
Generalized-Linear-Models
GLM
R
updated 20 hours ago by
Ram
43k • written 1 day ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
80
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
DoubletFinder
Seurat
modelHomotypic
updated 20 hours ago by
Ram
43k • written 1 day ago by
Jeyong
• 0
0
votes
2
replies
196
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
183
views
HaplotypeCaller - only SNPs
HaplotypeCaller
GATK
updated 1 day ago by
analyst
▴ 30 • written 1 day ago by
lorena9132
• 0
0
votes
0
replies
95
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
1 day ago by
Kash
▴ 110
7
votes
2
replies
247
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 1 day ago by
geneontologyhelp
▴ 390 • written 2 days ago by
catherine.teyssier
• 0
0
votes
1
reply
189
views
Blasting two protein sequences vs two nucleotide sequences
gene-hunting
blast
updated 1 day ago by
Istvan Albert
100k • written 2 days ago by
Abeer
• 0
0
votes
4
replies
270
views
Should I use unpaired reads from trimmomatic
RNA-seq
QC
Trimmomatic
updated 1 day ago by
swbarnes2
14k • written 2 days ago by
dxj294
• 0
0
votes
1
reply
133
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 1 day ago by
Mensur Dlakic
★ 27k • written 1 day ago by
benguyarenbeyaz98
• 0
0
votes
2
replies
223
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 20 hours ago by
Ram
43k • written 1 day ago by
v.berriosfarias
▴ 140
116,603 results • Page
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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
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Answer: What Is A "Spot" In Sra Format
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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…
Answer: Finding orthologs between genome error
by
Adrian Altenhoff
★ 1.1k
Hi, thanks for letting us know. In a recent software update, we introduced a problem with the written splice information in the cached …
Comment: Fetch table from clinvar database according to a list of rsid
by
ashaneev07
▴ 20
so which one should i prefer? i don't need the entire results i need the condition-Germline table only. (for eg:-from, https://www.ncbi.nlm…
Comment: To get p-values for the TPM
by
dsull
★ 5.8k
OK, not sure why your intention is to use RSEM p-values for, but at least tell us the commands you ran then otherwise how are we supposed t…
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