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1,000 results • Page
2 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
80
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
3 days ago by
feather-W
• 0
2
votes
4
replies
248
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
1 day ago by
samuelkalandarov2002
▴ 10
0
votes
0
replies
78
views
Annotating single cell data automatically
cell
annotation
single
3 days ago by
Gerard
• 0
0
votes
1
reply
144
views
RNA-seq bacteria contamination
RNA-seq
updated 3 days ago by
GenoMax
141k • written 3 days ago by
sh
• 0
0
votes
0
replies
70
views
Imputation advice
imputation
3 days ago by
kl
▴ 10
0
votes
0
replies
86
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
3 days ago by
Enrique
• 0
0
votes
0
replies
71
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
3 days ago by
sativus
▴ 20
0
votes
0
replies
78
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER
MARINA
ARACNe
3 days ago by
Biostars2200
• 0
0
votes
0
replies
125
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 3 days ago by
Carlo Yague
8.7k • written 3 days ago by
Atul K.
• 0
2
votes
5
replies
439
views
Marking duplicates using UMIs
Deduplication
UMI
updated 3 days ago by
i.sudbery
19k • written 4 days ago by
Lipika
• 0
0
votes
0
replies
138
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 4 days ago by
Ram
43k • written 4 days ago by
sainavyav22
• 0
0
votes
0
replies
138
views
Bacterial genome alignment with mauve
Bacteria
mauve
genome
4 days ago by
rthapa
▴ 90
0
votes
0
replies
132
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation
CGenFF
Gromacs
VMD
4 days ago by
Mamatha Y S
• 0
0
votes
2
replies
258
views
bam merging for archaic samples
samtools
bam
updated 4 days ago by
Ram
43k • written 5 days ago by
Matteo Ungaro
▴ 100
1
vote
0
replies
538
views
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers
TRINITY
5 days ago by
mathavanbioinfo
▴ 90
0
votes
0
replies
211
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
5 days ago by
abhishekghadge
• 0
2
votes
5
replies
681
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 4 days ago by
Jesse
▴ 740 • written 5 days ago by
Ann
★ 2.4k
0
votes
0
replies
186
views
agilent microarray gpl data does not have gene symbol column
microarray
agilent
gpl
updated 5 days ago by
Ram
43k • written 6 days ago by
mja
• 0
0
votes
0
replies
187
views
scRNA Cluster frequency
CV
PCA
scRNA
Cluster-Frequency
6 days ago by
Nitin
• 0
0
votes
0
replies
187
views
absolute path for symbolic links in Snakefile
Snakemake
updated 6 days ago by
Ram
43k • written 6 days ago by
yifangt86
▴ 60
0
votes
0
replies
180
views
Chemical structure validation
structure
cap
validation
metabolite
6 days ago by
Rodolfo Adrián
• 0
0
votes
1
reply
259
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 6 days ago by
GenoMax
141k • written 6 days ago by
bioyas
▴ 10
0
votes
0
replies
203
views
Copy number variation plot
Copy-number-variation
genomics
updated 6 days ago by
Ram
43k • written 6 days ago by
Emmi
• 0
0
votes
0
replies
177
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs
ngsTools
ANGSD
genomics
6 days ago by
DanielEB_fisk
▴ 20
0
votes
1
reply
280
views
Could you please assist in identifying this cluster?
single-cell
updated 6 days ago by
Ram
43k • written 6 days ago by
Kazo
• 0
0
votes
0
replies
194
views
Conversion to tree format
PLINK
bed
Figtree
SplitsTree
updated 6 days ago by
Ram
43k • written 6 days ago by
Dinmukhamed
• 0
0
votes
0
replies
193
views
miRDeep2: How to get the read counts
mirdeep2
6 days ago by
Atul K.
• 0
0
votes
0
replies
201
views
Lncipedia GTF file error
Proteomics
updated 6 days ago by
Ram
43k • written 6 days ago by
atharvakarkare14
▴ 10
3
votes
3
replies
466
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 5 days ago by
swbarnes2
14k • written 6 days ago by
joe
▴ 510
0
votes
2
replies
533
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
6 days ago by
航太郎
• 0
0
votes
0
replies
213
views
create genewise sync file in popoolation
popoolation
updated 6 days ago by
GenoMax
141k • written 6 days ago by
N.Y.Wiyana-Hewage
• 0
0
votes
2
replies
372
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
6 days ago by
Ashok
• 0
0
votes
2
replies
410
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
6 days ago by
Ashok
• 0
0
votes
0
replies
211
views
Variant Generation Using Longshot
long-reads
variant-calling
ONT
minion
longshot
updated 7 days ago by
Ram
43k • written 7 days ago by
samuelkalandarov2002
▴ 10
0
votes
2
replies
420
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
6 days ago by
_quantum_girl_
▴ 10
0
votes
0
replies
202
views
traying to make a maf from an already annotated vcf
vcf
vcf2maf
maf
maftools
VEP
3 days ago by
Javier
• 0
0
votes
0
replies
176
views
Pruning with plink finds a majority of SNPs in very high LD
LD
SNP
plink
pruning
7 days ago by
enferdeflame
• 0
1
vote
1
reply
412
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
updated 4 days ago by
Gordon Smyth
★ 7.0k • written 7 days ago by
Chris
▴ 260
0
votes
1
reply
398
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree
microbiome
updated 7 days ago by
Ram
43k • written 19 months ago by
Muhammad
• 0
0
votes
0
replies
157
views
How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau-score
tspex
updated 7 days ago by
Ram
43k • written 7 days ago by
bioinfo223
▴ 10
0
votes
0
replies
175
views
How to root an unrooted tree with a known root tree?
phylogenetics
rooting
R
7 days ago by
P.
• 0
0
votes
0
replies
166
views
Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
snpEff
7 days ago by
ekirsch
• 0
1
vote
1
reply
393
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
6 days ago by
renan.igor
• 0
0
votes
0
replies
174
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
7 days ago by
synat.keam
▴ 100
0
votes
1
reply
266
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 7 days ago by
GenoMax
141k • written 7 days ago by
ycts
• 0
0
votes
4
replies
574
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
6 days ago by
Kai Xin
• 0
1
vote
1
reply
223
views
Retrieve a % coverage for each transcript
RNA-seq
updated 8 days ago by
Ram
43k • written 8 days ago by
jammydodger123456
▴ 40
0
votes
2
replies
367
views
How can I solve this error?
metal
7 days ago by
22211020193
• 0
0
votes
0
replies
164
views
Struggling to lift genome builds
PLINK
liftover
GWAS
updated 8 days ago by
GenoMax
141k • written 8 days ago by
srimmer
• 0
1
vote
2
replies
270
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 8 days ago by
Ram
43k • written 8 days ago by
aniigodwinn
• 0
1,000 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?
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ScRNAseq-How to correctly choose cell type marker genes
ScRNA data question
Comment: SRA to BAM
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Recent Replies
Answer: why renaming Idents in Seurat object doesn't work?
by
Bioinfotec
▴ 10
I think when you give indent to seuObj : Idents(seuObj) <- 'RNA_snn_res.0.1' You may wrongly assign other value to it such as …
Answer: ScRNAseq-How to correctly choose cell type marker genes
by
Bioinfotec
▴ 10
In fact, there is no gold standard for cell type annotation. To achieve correct cell type classification, you can combine the two methos. F…
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by
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In violin plot, a dot represents a cell. Actually, the straight lines you see in your infected image just means these cells have the same e…
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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…
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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
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ginellegrenier
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Hi, I was wondering if you have found a solution to this? Thanks!
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cross posted in bioconductor. [https://support.bioconductor.org/p/9157968/][1] [1]: https://support.bioconductor.org/p/9157968/
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Which normalization method did you use for your data? I am guessing you had used SCTransform normalization for your data. Can you plot usin…
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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…
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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…
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the javascript in your html is deprecated or your firefox is just tool old.
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> 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 …
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