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1,000 results • Page
2 of 20
Sort: Rank
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Views
Votes
Replies
0
votes
0
replies
152
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
4 days ago by
Emily
▴ 10
1
vote
0
replies
165
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
4 days ago by
rohitsatyam102
▴ 850
0
votes
0
replies
151
views
how to read graph_test output of monocle 3
monocle3
4 days ago by
synat.keam
▴ 100
0
votes
1
reply
483
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 5 days ago by
ginellegrenier
• 0 • written 4 months ago by
Clayton
• 0
0
votes
0
replies
147
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
5 days ago by
Aspire
▴ 300
0
votes
3
replies
287
views
Highest variable features in single cell data
single-cell
updated 3 days ago by
bk11
★ 2.4k • written 5 days ago by
Kazo
▴ 10
1
vote
3
replies
347
views
PCA plot
DESeq2
PCAplot
updated 1 day ago by
LauferVA
4.2k • written 5 days ago by
Aaliya
▴ 10
0
votes
0
replies
145
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
5 days ago by
4fzcgueyp5
• 0
0
votes
2
replies
252
views
Annovar using R package
Annovar
gnomAD
R
4 days ago by
DKA
▴ 40
0
votes
5
replies
345
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 5 days ago by
GenoMax
141k • written 6 days ago by
Bertalan_Takacs
▴ 90
0
votes
0
replies
140
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 5 days ago by
Ram
43k • written 6 days ago by
glaciya2018
• 0
0
votes
0
replies
306
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
6 days ago by
pramach1
▴ 40
0
votes
1
reply
161
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 6 days ago by
Sofia
• 0 • written 6 days ago by
mawigoj318
• 0
0
votes
0
replies
142
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
6 days ago by
salias
• 0
0
votes
5
replies
345
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 3 days ago by
Istvan Albert
100k • written 6 days ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
121
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 5 days ago by
Ram
43k • written 6 days ago by
newuser2024
• 0
1
vote
2
replies
231
views
alignment result
RNA-seq
samtools
hisat2
5 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
105
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
DoubletFinder
Seurat
modelHomotypic
updated 5 days ago by
Ram
43k • written 6 days ago by
Jeyong
• 0
0
votes
0
replies
113
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
6 days ago by
Kash
▴ 110
0
votes
1
reply
157
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 6 days ago by
Mensur Dlakic
★ 27k • written 6 days ago by
benguyarenbeyaz98
• 0
2
votes
2
replies
276
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 5 days ago by
Ram
43k • written 6 days ago by
v.berriosfarias
▴ 140
2
votes
9
replies
854
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 6 days ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
0
votes
11
replies
537
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
4 days ago by
atowns21
• 0
0
votes
1
reply
166
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 6 days ago by
bk11
★ 2.4k • written 6 days ago by
alphaflylizard
• 0
0
votes
0
replies
101
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
7 days ago by
ohtang7
▴ 40
0
votes
1
reply
168
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 7 days ago by
GenoMax
141k • written 7 days ago by
Srinka
▴ 20
0
votes
5
replies
327
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
6 days ago by
njornet
▴ 20
0
votes
0
replies
96
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 7 days ago by
Ram
43k • written 7 days ago by
SHREYA
• 0
0
votes
0
replies
103
views
Merging replicates from Encode project
CHIP-seq
encode
7 days ago by
Nurken
• 0
1
vote
3
replies
239
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
7 days ago by
WouterDeCoster
47k
1
vote
3
replies
277
views
some error in building kraken2 database
metagenome
kraken2
6 days ago by
Art1ess
• 0
0
votes
1
reply
156
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 7 days ago by
bk11
★ 2.4k • written 7 days ago by
Susmita Mandal
▴ 110
1
vote
1
reply
177
views
Failed kmer content
kmer
illumina
ngs
updated 7 days ago by
Ram
43k • written 7 days ago by
Kasturi
• 0
0
votes
0
replies
93
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 7 days ago by
Ram
43k • written 7 days ago by
SSSJec
• 0
0
votes
1
reply
150
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 7 days ago by
Ram
43k • written 7 days ago by
Cameron.walker9900
• 0
0
votes
8
replies
343
views
Error in cnetplot enrichplot package
R
updated 7 days ago by
Ram
43k • written 7 days ago by
Farhad
• 0
0
votes
0
replies
112
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 7 days ago by
Ram
43k • written 7 days ago by
maxime.policarpo
▴ 200
0
votes
0
replies
96
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 7 days ago by
Ram
43k • written 7 days ago by
sansan_96
▴ 80
0
votes
0
replies
102
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 7 days ago by
Ram
43k • written 7 days ago by
Amélie
• 0
0
votes
0
replies
204
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 7 days ago by
Ram
43k • written 7 days ago by
Oak
▴ 10
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink
PED
updated 7 days ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
1
vote
7
replies
365
views
Downsampling fastq file
downsample
fastq
updated 1 day ago by
Ram
43k • written 7 days ago by
marco.barr
▴ 80
0
votes
1
reply
140
views
tbtool
tbtool
updated 7 days ago by
Ram
43k • written 8 days ago by
Raman
• 0
0
votes
10
replies
440
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 6 hours ago by
i.sudbery
19k • written 8 days ago by
Patadu94
• 0
0
votes
1
reply
133
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 8 days ago by
ATpoint
82k • written 8 days ago by
enanoide
• 0
0
votes
0
replies
91
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
8 days ago by
manaswwm
▴ 510
0
votes
0
replies
82
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
7 days ago by
alifafiq1
• 0
0
votes
0
replies
87
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
8 days ago by
feather-W
• 0
2
votes
4
replies
298
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
6 days ago by
samuelkalandarov2002
▴ 10
0
votes
0
replies
87
views
Annotating single cell data automatically
cell
annotation
single
8 days ago by
Gerard
• 0
1,000 results • Page
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Programmatically retrieving positions of protein active site residues
Answer: Polishing genome assembly
Answer: Integrate transcriptomic data and proteomics data.
Answer: Integrate transcriptomic data and proteomics data.
Comment: Integrate transcriptomic data and proteomics data.
Comment: Integrate transcriptomic data and proteomics data.
Answer: Is it possible to bulk download files from GEO repository?
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Recent Replies
Comment: KEGG Pathways
by
Ram
43k
> is the below code correct Does it give you what you need?
Comment: from row count to tpm
by
Ram
43k
Hi https://www.biostars.org/u/119503/ Why did you delete this post?
Comment: ERROR When Using Ensembl Plants Biomart Wget API
by
GenoMax
141k
A couple of hours back using `plants.ensembl.org` was generating a 504 error but it seems to be working now. wget -O result.txt 'http…
Comment: why renaming Idents in Seurat object doesn't work?
by
Assa Yeroslaviz
★ 1.8k
Don't understand this comment. I don't have any columns with this name.
Answer: ERROR When Using Ensembl Plants Biomart Wget API
by
Ben_Ensembl
★ 2.4k
Hi Dora, For plant species such as *A. thalina*, you should use the http://plants.ensembl.org/biomart service, so the start of your wget…
Answer: Introduce SNPs on FASTA
by
christopher medway
▴ 450
You could take a look at the mutfa command in [seqtk][1] [1]: https://docs.csc.fi/apps/seqtk/#usage
Answer: Introduce SNPs on FASTA
by
Michael
54k
If you have a VCF file with all the ALT alleles that you need to insert and a reference genome in FASTA, you can use [bcftools consensus][1…
Comment: Introduce SNPs on FASTA
by
Riccardo
▴ 10
Thank you very much. Is there a script or program that does it automatically?
Comment: Post-imputation plot
by
kl
▴ 10
This does not warrant redoing the imputation, though? Do you have any advice of what to take care of, in this circumstance? Thanks!
Comment: unable to get feature count results
by
GenoMax
141k
Galaxy specific questions are best posted to their support site: https://help.galaxyproject.org/ That said, problems with counting are lik…
Comment: Landmark gene selection in L1000.
by
GenoMax
141k
Link for the data is included above.
Comment: Introduce SNPs on FASTA
by
GenoMax
141k
If you have specific changes you want to make then you can edit the fasta file accordingly.
Answer: Taking the difference of two VCFs (or removing singletons)
by
Andres
▴ 20
I know this is an old question but when searching for filtering out singletons(and doubletons too) i found this post in the first results. …
Comment: NGS forensics: how to know if data is fabricated
by
i.sudbery
19k
In which case, I'd definately look at the distribution of read lengths, post trimming, and see if there is a discontinuity in the distribut…
Comment: Low mapping rate with Salmon
by
i.sudbery
19k
I would note that even on a good, polyA selected, RNA-seq run, I would only expect 60-75% of mapped reads to map to protein coding exons.
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