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397 results • Page
5 of 8
Sort: Rank
Rank
Views
Votes
Replies
0
votes
2
replies
308
views
Annovar using R package
Annovar
gnomAD
R
19 days ago by
DKA
▴ 40
0
votes
5
replies
437
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 20 days ago by
GenoMax
142k • written 21 days ago by
Bertalan_Takacs
▴ 90
0
votes
0
replies
166
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 21 days ago by
Ram
43k • written 21 days ago by
glaciya2018
• 0
0
votes
0
replies
328
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
21 days ago by
pramach1
▴ 40
0
votes
1
reply
204
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 21 days ago by
Sofia
• 0 • written 21 days ago by
mawigoj318
• 0
0
votes
0
replies
167
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
21 days ago by
salias
• 0
0
votes
5
replies
455
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 18 days ago by
Istvan Albert
100k • written 21 days ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
141
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 21 days ago by
Ram
43k • written 21 days ago by
newuser2024
• 0
1
vote
2
replies
280
views
alignment result
RNA-seq
samtools
hisat2
20 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
139
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
21 days ago by
Kash
▴ 110
0
votes
1
reply
189
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 21 days ago by
Mensur Dlakic
★ 27k • written 21 days ago by
benguyarenbeyaz98
• 0
2
votes
2
replies
334
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 21 days ago by
Ram
43k • written 21 days ago by
v.berriosfarias
▴ 140
2
votes
9
replies
936
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 21 days ago by
LauferVA
4.2k • written 7 months ago by
Gnana
• 0
0
votes
11
replies
704
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
19 days ago by
atowns21
• 0
0
votes
1
reply
211
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 22 days ago by
bk11
★ 2.4k • written 22 days ago by
alphaflylizard
• 0
0
votes
0
replies
119
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
22 days ago by
ohtang7
▴ 40
0
votes
1
reply
205
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 22 days ago by
GenoMax
142k • written 22 days ago by
Srinka
▴ 20
0
votes
5
replies
424
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
21 days ago by
njornet
▴ 20
0
votes
0
replies
124
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 22 days ago by
Ram
43k • written 22 days ago by
SHREYA
• 0
0
votes
0
replies
126
views
Merging replicates from Encode project
CHIP-seq
encode
22 days ago by
Nurken
• 0
1
vote
3
replies
299
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
22 days ago by
WouterDeCoster
47k
1
vote
3
replies
333
views
some error in building kraken2 database
metagenome
kraken2
21 days ago by
Art1ess
• 0
0
votes
1
reply
209
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 22 days ago by
bk11
★ 2.4k • written 22 days ago by
Susmita Mandal
▴ 110
1
vote
1
reply
210
views
Failed kmer content
kmer
illumina
ngs
updated 22 days ago by
Ram
43k • written 22 days ago by
Kasturi
• 0
0
votes
0
replies
115
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 22 days ago by
Ram
43k • written 22 days ago by
SSSJec
• 0
0
votes
1
reply
174
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 22 days ago by
Ram
43k • written 23 days ago by
Cameron.walker9900
• 0
0
votes
8
replies
453
views
Error in cnetplot enrichplot package
R
updated 22 days ago by
Ram
43k • written 23 days ago by
Farhad
• 0
0
votes
0
replies
128
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 23 days ago by
Ram
43k • written 23 days ago by
maxime.policarpo
▴ 200
0
votes
0
replies
113
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 23 days ago by
Ram
43k • written 23 days ago by
sansan_96
▴ 90
0
votes
0
replies
115
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 22 days ago by
Ram
43k • written 23 days ago by
Amélie
• 0
0
votes
0
replies
222
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 23 days ago by
Ram
43k • written 23 days ago by
Pine
▴ 20
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink
PED
updated 22 days ago by
chrchang523
10k • written 6.2 years ago by
Ginevra
▴ 10
1
vote
8
replies
531
views
Downsampling fastq file
downsample
fastq
15 days ago by
marco.barr
▴ 110
0
votes
1
reply
168
views
tbtool
tbtool
updated 23 days ago by
Ram
43k • written 23 days ago by
Raman
• 0
0
votes
10
replies
605
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 15 days ago by
i.sudbery
19k • written 23 days ago by
Patadu94
• 0
0
votes
1
reply
158
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 23 days ago by
ATpoint
82k • written 23 days ago by
enanoide
• 0
0
votes
0
replies
105
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
23 days ago by
manaswwm
▴ 510
0
votes
0
replies
96
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
22 days ago by
alifafiq1
• 0
0
votes
0
replies
102
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
23 days ago by
feather-W
• 0
2
votes
4
replies
375
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
21 days ago by
samuelkalandarov2002
▴ 10
0
votes
0
replies
98
views
Annotating single cell data automatically
cell
annotation
single
23 days ago by
Gerard
• 0
0
votes
1
reply
199
views
RNA-seq bacteria contamination
RNA-seq
updated 23 days ago by
GenoMax
142k • written 23 days ago by
sh
• 0
0
votes
0
replies
95
views
Imputation advice
imputation
23 days ago by
kl
▴ 10
0
votes
0
replies
117
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
23 days ago by
Enrique
• 0
0
votes
0
replies
91
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
23 days ago by
sativus
▴ 20
0
votes
0
replies
96
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER
MARINA
ARACNe
23 days ago by
Biostars2200
• 0
0
votes
0
replies
155
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 23 days ago by
Carlo Yague
8.7k • written 23 days ago by
Atul K.
• 0
2
votes
5
replies
528
views
Marking duplicates using UMIs
Deduplication
UMI
updated 23 days ago by
i.sudbery
19k • written 24 days ago by
Lipika
• 0
0
votes
0
replies
156
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 24 days ago by
Ram
43k • written 24 days ago by
sainavyav22
• 0
0
votes
0
replies
161
views
Bacterial genome alignment with mauve
Bacteria
mauve
genome
24 days ago by
rthapa
▴ 90
397 results • Page
5 of 8
Recent Votes
Answer: Doubt about the process of annotation, detection, identification and classificat
Answer: Filtering VCF files based on VAF giving incorrect results
Problems with breakdancer (sv caller) output.
Problems with breakdancer (sv caller) output.
Comment: Add stats to boxplot in R
Answer: Genotyping sites with N in reference genome
A: how to combine RNA seq data from 4 lanes
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Recent Replies
Comment: Filtering VCF files based on VAF giving incorrect results
by
Arton
• 0
Thank you. I can't try a completely new tool but I will keep your command for future use. Do you think my commands were correct? For exampl…
Comment: Add stats to boxplot in R
by
Ghada
• 0
Thanks. Thats work
Comment: Genotyping sites with N in reference genome
by
Zhenyu Zhang
★ 1.2k
Whether N -> A/T/G/C represents a variant is heavily dependent on the tool itself, and I know most tools don't. Since you don't see it in y…
Comment: calculating genomic coverage/ base overlap in R
by
marco.barr
▴ 110
The code seems correct at first glance... How did you generate the data in the Excel file? Have you checked the exon annotations? You could…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Did you remeber to unzip/untar the `nt` preformatted files that you downloaded?
Comment: Genotyping sites with N in reference genome
by
shpak.max
▴ 50
Just to clarify, I have set additional sites in the reference genome to 'N', which means (based on your statement) that these will not be g…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
Pierre Lindenbaum
161k
see https://www.biostars.org/p/9496674/ <!-- when i runed blastn(version 2.15) and nt database(latest version). I used aspera to download…
Answer: Genotyping sites with N in reference genome
by
Pierre Lindenbaum
161k
> Does UnifiedGenotyper skip/ignore sites where the reference genotype is N yes. The variant is in YOUR data, not in the reference where '…
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline?
by
yura.grabovska
▴ 70
Do you have samples that should in theory have a good degree over overlap in terms of cell types across the two sequencing types? I would …
Comment: Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
by
asalimih
▴ 60
I found out that vep is only checking the GT field therefore assigning HOM to the Zygosity. Therefore the problem should be from deepvarian…
Comment: Add stats to boxplot in R
by
Lélé
▴ 10
To remove "Kruskall Wallis" you can try adding the argument label="p" or label = "p.signif" which displays the p-value or *** like this: …
Answer: Sequencing Depth (Read Depth) Calculations
by
GenoMax
142k
You could also use `pandepth` ([**LINK**][1]) or `mosdepth` ([**LINK**][2]) as well. These will allow you to be flexible about windowed cov…
Comment: Sequencing Depth (Read Depth) Calculations
by
Pierre Lindenbaum
161k
it looks looks ok to me. <!-- This cmd works and gives me 40.5235, I was wondering whether this cmd is right or wrong, and does anyone hav…
Comment: Add stats to boxplot in R
by
Ghada
• 0
Great. thats work. Do you know how can I remove the kruskall-Wallis name from the plot? Also I would like to draw a line under the kruskall…
Comment: Using ggplotly in R
by
jared.andrews07
★ 16k
Again, this is not particularly difficult to do with [plotly itself](https://plotly.com/r/line-and-scatter/#adding-color-and-size-mapping) …
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