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89 results • Page
2 of 2
Sort: Rank
Rank
Views
Votes
Replies
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
342
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 4 days ago by
GenoMax
141k • written 5 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 5 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
5 days ago by
pramach1
▴ 40
0
votes
1
reply
157
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 5 days ago by
Sofia
• 0 • written 5 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
343
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 2 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
104
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
274
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
852
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
535
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
165
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
6 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 6 days ago by
GenoMax
141k • written 6 days ago by
Srinka
▴ 20
0
votes
5
replies
326
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
5 days ago by
njornet
▴ 20
0
votes
0
replies
95
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 6 days ago by
Ram
43k • written 6 days ago by
SHREYA
• 0
0
votes
0
replies
102
views
Merging replicates from Encode project
CHIP-seq
encode
6 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
6 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
154
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 6 days ago by
bk11
★ 2.4k • written 7 days ago by
Susmita Mandal
▴ 110
1
vote
1
reply
176
views
Failed kmer content
kmer
illumina
ngs
updated 6 days ago by
Ram
43k • written 7 days ago by
Kasturi
• 0
0
votes
0
replies
92
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 6 days ago by
Ram
43k • written 7 days ago by
SSSJec
• 0
0
votes
0
replies
102
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 6 days ago by
Ram
43k • written 7 days ago by
Amélie
• 0
1
vote
7
replies
363
views
Downsampling fastq file
downsample
fastq
updated 19 hours ago by
Ram
43k • written 7 days ago by
marco.barr
▴ 80
0
votes
10
replies
382
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 41 minutes ago by
i.sudbery
19k • written 7 days ago by
Patadu94
• 0
0
votes
0
replies
81
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
6 days ago by
alifafiq1
• 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
6
replies
449
views
Use of Kraken output for functional analysis
metagenomics
kraken
shotgun
updated 6 days ago by
gv
• 0 • written 28 days ago by
Srinka
▴ 20
0
votes
3
replies
311
views
CWl and toil singularity image e.g busybox? Thank you
toil
singularity
updated 19 hours ago by
Ram
43k • written 4 months ago by
Fadi
• 0
2
votes
5
replies
917
views
Retrieval of Active site information programmatically
Catalytic
Python
Active
PDB
site
Site
updated 17 hours ago by
Wayne
★ 2.0k • written 2.0 years ago by
arinjoy
• 0
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference
38build
impute
imputation
16 hours ago by
anna
▴ 20
1
vote
6
replies
2.8k
views
Segmentation fault using gemma
gemma
gwas
updated 22 hours ago by
dimpleadiwal050896
• 0 • written 4.9 years ago by
ggman
▴ 90
89 results • Page
2 of 2
Recent Votes
Comment: NGS forensics: how to know if data is fabricated
Answer: blasting genome contigs against local SILVA 16S RNA database
blasting genome contigs against local SILVA 16S RNA database
Comment: Integrate transcriptomic data and proteomics data.
Comment: MA plot of shrunken fold change
Comment: Need help for downloading arabdopsis thaliana reference genome fasta file and gt
Answer: How to find rna strand direction before alignment?
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82k
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Recent Replies
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.
Answer: FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last plac
by
David Langenberger
11k
:: FINAL CALL :: 8th Berlin Summer School in NGS Data Analysis 2024 - Only a few last places available
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
Oh, then I will check the output file from featureCounts.
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
How would I check if these reads are aligning to regions where there is no expressed sequence know? Should I follow the suggestion of i.sud…
Answer: Deseq2
by
Jack Tierney
▴ 360
[This vignette][1] is a great place to start. [1]: https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.ht…
Comment: Genbank File Format
by
alenew.am
• 0
Thanks, yes i have tried first here looking for a easier solution (for me), i didnt' know if this format was already available somewhere. t…
Comment: Genbank File Format
by
alenew.am
• 0
Yes, it would be fine with an external solution, thanks for the reply
Answer: Polishing genome assembly
by
Michael
54k
If you have Hifi reads your error rate should already be quite good, therefore polishing with potentially longer and slightly more error-pr…
Comment: Integrate transcriptomic data and proteomics data.
by
Lluís R.
★ 1.2k
You don't need to subset for common features, there are tools that work for that like RGCCA, mixOmics. See for instance a classification [h…
Answer: Integrate transcriptomic data and proteomics data.
by
KABILAN
▴ 50
You can use R package named 'mixOmics' to integrate the datasets. Kindly go through the manual of this package.
Comment: Need help for downloading arabdopsis thaliana reference genome fasta file and gt
by
Michael
54k
You will have to describe your problem in much more detail, we are unable to understand what the problem even is. > Please, anyone, sugge…
Comment: MA plot of shrunken fold change
by
Sudip
• 0
Thank you.
Comment: MA plot of shrunken fold change
by
ATpoint
82k
You will need to relevel to make all comparisons available as coefficients, see https://www.biostars.org/p/448959/, or just use ashr shrink…
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