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93 results • Page
2 of 2
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Views
Votes
Replies
0
votes
0
replies
81
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 2 days ago by
Ram
43k • written 2 days ago by
SSSJec
• 0
0
votes
1
reply
146
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 2 days ago by
bk11
★ 2.3k • written 2 days ago by
alphaflylizard
• 0
0
votes
0
replies
102
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
1 day ago by
Kash
▴ 110
0
votes
10
replies
397
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
1 day ago by
atowns21
• 0
0
votes
1
reply
138
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
6
replies
424
views
Use of Kraken output for functional analysis
metagenomics
kraken
shotgun
updated 1 day ago by
gv
• 0 • written 24 days ago by
Srinka
▴ 20
0
votes
0
replies
110
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
1 day ago by
salias
• 0
0
votes
5
replies
280
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
1 day ago by
njornet
▴ 20
0
votes
0
replies
201
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
1
reply
125
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
108
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 1 day ago by
Ram
43k • written 1 day ago by
glaciya2018
• 0
0
votes
0
replies
99
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 1 day ago by
Ram
43k • written 1 day ago by
newuser2024
• 0
0
votes
0
replies
90
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
DoubletFinder
Seurat
modelHomotypic
updated 1 day ago by
Ram
43k • written 1 day ago by
Jeyong
• 0
0
votes
2
replies
227
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 1 day ago by
Ram
43k • written 1 day ago by
v.berriosfarias
▴ 140
0
votes
1
reply
135
views
Annovar using R package
Annovar
gnomAD
R
updated 21 hours ago by
Pierre Lindenbaum
161k • written 1 day ago by
DKA
▴ 40
0
votes
0
replies
82
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
19 hours ago by
4fzcgueyp5
• 0
0
votes
4
replies
234
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
11 hours ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
55
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
11 hours ago by
Aspire
▴ 300
0
votes
2
replies
133
views
Highest variable features in single cell data
cell
single
10 hours ago by
Kazo
• 0
0
votes
5
replies
259
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 7 hours ago by
GenoMax
141k • written 1 day ago by
Bertalan_Takacs
▴ 90
0
votes
1
reply
121
views
PCA plot
DESeq2
PCAplot
updated 5 hours ago by
jkim
▴ 170 • written 17 hours ago by
Aaliya
▴ 10
0
votes
1
reply
369
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 5 hours ago by
ginellegrenier
• 0 • written 4 months ago by
Clayton
• 0
0
votes
0
replies
35
views
how to read graph_test output of monocle 3
monocle3
4 hours ago by
synat.keam
▴ 100
0
votes
0
replies
38
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
3 hours ago by
rohitsatyam102
▴ 840
0
votes
0
replies
31
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
3 hours ago by
Emily
▴ 10
0
votes
0
replies
34
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
3 hours ago by
avocado123
• 0
0
votes
2
replies
537
views
autodockvina
python
python3
autodock
updated 6 days ago by
Ram
43k • written 4 months ago by
iamsmor
• 0
0
votes
1
reply
22
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 19 minutes ago by
ATpoint
82k • written 54 minutes ago by
AaronJaime
• 0
0
votes
0
replies
213
views
create genewise sync file in popoolation
popoolation
updated 6 days ago by
GenoMax
141k • written 7 days ago by
N.Y.Wiyana-Hewage
• 0
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
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
4
replies
575
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
6 days ago by
Kai Xin
• 0
0
votes
0
replies
194
views
miRDeep2: How to get the read counts
mirdeep2
6 days ago by
Atul K.
• 0
0
votes
0
replies
178
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs
ngsTools
ANGSD
genomics
6 days ago by
DanielEB_fisk
▴ 20
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
1
reply
281
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
195
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
201
views
Lncipedia GTF file error
Proteomics
updated 6 days ago by
Ram
43k • written 6 days ago by
atharvakarkare14
▴ 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
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
187
views
absolute path for symbolic links in Snakefile
Snakemake
updated 6 days ago by
Ram
43k • written 6 days ago by
yifangt86
▴ 60
93 results • Page
2 of 2
Recent Votes
Detecting somatic variants in non-tumor tissue without normals
Answer: Sequence read length shorter than flow cell specification
Answer: Sequence read length shorter than flow cell specification
Comment: Why gatk VariantAnnotator required bam and coverage files
A: Generate Vcf.Gz File And Its Index File Vcf.Gz.Tbi
Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
Answer: How do I get the 3bp sequence on either side of a co-ordinate
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Recent Replies
Comment: Treatment VS Control in Single Cell RNAseq analysis
by
ATpoint
82k
Open a new question, with details.
Comment: Normalize scRNAseq data to housekeeping genes to compare several datasets
by
ATpoint
82k
I recommend https://bioconductor.org/books/3.18/OSCA.basic/normalization.html as well as the "advanced" section in this book.
Comment: Why gatk VariantAnnotator required bam and coverage files
by
QX
• 0
thank you!
Comment: Treatment VS Control in Single Cell RNAseq analysis
by
kilcdincer
▴ 10
Hello, I have more or less same experimental setting and was wondering how you proceeded with your analysis? Can I reach its GitHub reposit…
Comment: BLAST using both nucleotides and taxonomic local databases
by
GenoMax
141k
> I ask this as some BLAST command fields as scinames or sblastnames do not give any output with a classic nt BLAST If that information is…
Answer: BLAST using both nucleotides and taxonomic local databases
by
5heikki
11k
This has been discussed [many times][1] [1]: https://www.biostars.org/p/76551/
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…
Answer: ScRNA data question
by
Bioinfotec
▴ 10
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…
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/
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