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109 results • Page
1 of 3
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0
votes
0
replies
6
views
how to read graph_test output of monocle 3
monocle3
7 minutes ago by
synat.keam
▴ 100
0
votes
1
reply
344
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
47
views
ScRNA data question
scRNA
Vlnplot
Samples
updated 1 hour ago by
bk11
★ 2.3k • written 2 hours ago by
starswillfade
▴ 10
1
vote
0
replies
36
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell
markers
2 hours ago by
Francesco
▴ 10
0
votes
0
replies
38
views
Calling SE and TE using ROSE
Calling
SE
3 hours ago by
Manhezz
• 0
0
votes
0
replies
48
views
BLAST using both nucleotides and taxonomic local databases
blast
ncbi
taxid
taxonomy
4 hours ago by
Begonia_pavonina
▴ 150
2
votes
3
replies
92
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
updated 30 minutes ago by
Pierre Lindenbaum
161k • written 5 hours ago by
QX
• 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
0
votes
2
replies
120
views
Highest variable features in single cell data
cell
single
5 hours ago by
Kazo
• 0
0
votes
1
reply
91
views
PCA plot
DESeq2
PCAplot
updated 1 hour ago by
jkim
▴ 170 • written 12 hours ago by
Aaliya
▴ 10
0
votes
0
replies
75
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
15 hours ago by
4fzcgueyp5
• 0
0
votes
1
reply
129
views
Annovar using R package
Annovar
gnomAD
R
updated 17 hours ago by
Pierre Lindenbaum
161k • written 20 hours ago by
DKA
▴ 40
0
votes
5
replies
236
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
101
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
174
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
118
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
0
votes
4
replies
222
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
7 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 21 hours ago by
Ram
43k • written 1 day ago by
newuser2024
• 0
1
vote
2
replies
170
views
alignment result
RNA-seq
samtools
hisat2
10 hours ago by
ahmad.sajad4541
• 0
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
0
replies
96
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
1 day ago by
Kash
▴ 110
0
votes
1
reply
134
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
225
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 21 hours ago by
Ram
43k • written 1 day ago by
v.berriosfarias
▴ 140
2
votes
9
replies
809
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 1 day ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
0
votes
10
replies
387
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
143
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 1 day ago by
bk11
★ 2.3k • written 1 day ago by
alphaflylizard
• 0
0
votes
0
replies
90
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
2 days ago by
ohtang7
▴ 40
0
votes
1
reply
148
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 2 days ago by
GenoMax
141k • written 2 days ago by
Srinka
▴ 20
0
votes
5
replies
279
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
84
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 2 days ago by
Ram
43k • written 2 days ago by
SHREYA
• 0
0
votes
0
replies
93
views
Merging replicates from Encode project
CHIP-seq
encode
2 days ago by
Nurken
• 0
1
vote
3
replies
197
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
2 days ago by
WouterDeCoster
47k
1
vote
3
replies
234
views
some error in building kraken2 database
metagenome
kraken2
1 day ago by
Art1ess
• 0
0
votes
1
reply
125
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 2 days ago by
bk11
★ 2.3k • written 2 days ago by
Susmita Mandal
▴ 110
1
vote
1
reply
160
views
Failed kmer content
kmer
illumina
ngs
updated 2 days ago by
Ram
43k • written 2 days ago by
Kasturi
• 0
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
138
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 2 days ago by
Ram
43k • written 2 days ago by
Cameron.walker9900
• 0
0
votes
8
replies
290
views
Error in cnetplot enrichplot package
R
updated 2 days ago by
Ram
43k • written 2 days ago by
Farhad
• 0
0
votes
0
replies
104
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 2 days ago by
Ram
43k • written 2 days ago by
maxime.policarpo
▴ 200
0
votes
0
replies
88
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 2 days ago by
Ram
43k • written 2 days ago by
sansan_96
▴ 80
0
votes
0
replies
92
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 2 days ago by
Ram
43k • written 2 days ago by
Amélie
• 0
0
votes
0
replies
170
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 2 days ago by
Ram
43k • written 2 days ago by
Oak
▴ 10
1
vote
3
replies
2.4k
views
Problem to remove subset of patients with plink
plink
PED
updated 2 days ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
1
vote
5
replies
250
views
Downsampling fastq file
downsample
fastq
updated 2 days ago by
Ram
43k • written 3 days ago by
marco.barr
▴ 80
0
votes
1
reply
124
views
tbtool
tbtool
updated 3 days ago by
Ram
43k • written 3 days ago by
Raman
• 0
0
votes
2
replies
186
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 2 days ago by
i.sudbery
19k • written 3 days ago by
Patadu94
• 0
0
votes
1
reply
118
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 3 days ago by
ATpoint
82k • written 3 days ago by
enanoide
• 0
0
votes
0
replies
82
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
3 days ago by
manaswwm
▴ 490
0
votes
0
replies
73
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
2 days ago by
alifafiq1
• 0
109 results • Page
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Answer: How do I get the 3bp sequence on either side of a co-ordinate
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What is the difference between HaplotypeCaller and UnifiedGenotyper?
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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
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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 …
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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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Hi, thanks for letting us know. In a recent software update, we introduced a problem with the written splice information in the cached …
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▴ 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…
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