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109 results • Page
2 of 3
Sort: Views
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Views
Votes
Replies
0
votes
0
replies
203
views
Copy number variation plot
Copy-number-variation
genomics
updated 5 days ago by
Ram
43k • written 6 days ago by
Emmi
• 0
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
201
views
Lncipedia GTF file error
Proteomics
updated 6 days ago by
Ram
43k • written 6 days ago by
atharvakarkare14
▴ 10
1
vote
3
replies
194
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
2 days ago by
WouterDeCoster
47k
0
votes
0
replies
193
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
187
views
absolute path for symbolic links in Snakefile
Snakemake
updated 5 days ago by
Ram
43k • written 5 days ago by
yifangt86
▴ 60
0
votes
0
replies
186
views
scRNA Cluster frequency
CV
PCA
scRNA
Cluster-Frequency
5 days ago by
Nitin
• 0
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 5 days ago by
mja
• 0
0
votes
2
replies
184
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
0
replies
180
views
Chemical structure validation
structure
cap
validation
metabolite
5 days ago by
Rodolfo Adrián
• 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
0
replies
172
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
0
replies
169
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
2
replies
167
views
alignment result
RNA-seq
samtools
hisat2
9 hours ago by
ahmad.sajad4541
• 0
1
vote
1
reply
159
views
Failed kmer content
kmer
illumina
ngs
updated 2 days ago by
Ram
43k • written 2 days ago by
Kasturi
• 0
0
votes
1
reply
147
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
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
1
reply
142
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
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
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
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
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
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
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
0
votes
1
reply
124
views
tbtool
tbtool
updated 2 days ago by
Ram
43k • written 3 days ago by
Raman
• 0
0
votes
1
reply
124
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
0
votes
2
replies
118
views
Highest variable features in single cell data
cell
single
5 hours ago by
Kazo
• 0
0
votes
1
reply
117
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
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
103
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
102
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
1 day ago by
salias
• 0
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
94
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
1 day ago by
Kash
▴ 110
0
votes
0
replies
92
views
Merging replicates from Encode project
CHIP-seq
encode
2 days ago by
Nurken
• 0
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
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
0
votes
0
replies
89
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
2 days ago by
ohtang7
▴ 40
0
votes
0
replies
87
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
1
reply
87
views
PCA plot
DESeq2
PCAplot
updated 1 hour ago by
jkim
▴ 170 • written 12 hours ago by
Aaliya
▴ 10
0
votes
0
replies
86
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
3 days ago by
Enrique
• 0
2
votes
3
replies
85
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
updated just now by
Pierre Lindenbaum
161k • written 5 hours ago by
QX
• 0
0
votes
0
replies
83
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
82
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
3 days ago by
manaswwm
▴ 490
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
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
0
votes
0
replies
80
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
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
78
views
Annotating single cell data automatically
cell
annotation
single
3 days ago by
Gerard
• 0
109 results • Page
2 of 3
Recent Votes
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
Answer: What Is A "Spot" In Sra Format
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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…
Comment: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
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