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1,000 results • Page
4 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
2
replies
275
views
RNAseq 1 control 2 different treatment
RNA-seq
13 days ago by
matteo.levorato
• 0
1
vote
0
replies
146
views
Seeking Advice on Gene Ontology Analysis for Bulk RNA-Seq Data Without Control Samples
Gene-ontology
RNA-seq
R
updated 13 days ago by
Ram
43k • written 13 days ago by
Oscar
▴ 10
0
votes
0
replies
158
views
How should I make kallisto indexes?
kallisto
updated 13 days ago by
GenoMax
141k • written 13 days ago by
bioinfo
▴ 150
2
votes
0
replies
211
views
What are good Python models/packages to predict small molecula (SMILES) binding to proteins ?
SMILES
14 days ago by
Alexander
▴ 220
1
vote
1
reply
186
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 14 days ago by
GenoMax
141k • written 14 days ago by
eesiribloom
▴ 80
0
votes
0
replies
141
views
Automated internal stop codon checker
ORF
stopcodon
internal
virus
14 days ago by
Balazs Horvath
▴ 10
0
votes
0
replies
146
views
Repeat expansion identification tools for long-read data
fragilex
repeatexpansion
long-read
fmr1
14 days ago by
adarsh_pp
▴ 40
0
votes
0
replies
155
views
FreeBayes detection capacity
reads
freebayes
long
14 days ago by
quentinperriere
• 0
0
votes
2
replies
260
views
VCF annotation with gnomADv4 using R package
annotation
gnomADv4
R
VCF
12 days ago by
DKA
▴ 40
0
votes
0
replies
166
views
Plotting heatmap of genes in each samples scRNA in Seurat
scRNA
heatmap
14 days ago by
Hien
• 0
0
votes
2
replies
300
views
Merging Outputs from plink --assoc and --hardy to Produce Table
PLINK
PANDAS
R
12 days ago by
Koketso
• 0
0
votes
0
replies
194
views
Novel cyclic peptide structure prediction
protein
structure-prediction
alphafold
peptide
updated 14 days ago by
Ram
43k • written 15 days ago by
menyawino
• 0
1
vote
3
replies
362
views
Ensembl gene id conversion
biomart
ensembl
updated 13 days ago by
ATpoint
82k • written 15 days ago by
naveedhasan2000
• 0
1
vote
2
replies
323
views
Extracting information from gff3 file produced by augustus
augustus
gff3
updated 13 days ago by
Istvan Albert
100k • written 15 days ago by
Jiang
• 0
0
votes
0
replies
196
views
Core SNP tree VS. concatenated core genome tree
phylogenetic
tree
SNP
16 days ago by
YiweiZhu
▴ 30
0
votes
2
replies
322
views
Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics
metacyc
enzyme
biobakery
humann
15 days ago by
O.rka
▴ 710
0
votes
6
replies
559
views
PacBio adapters in transcriptome assembly from short read data?
adapter
transcriptome
sequencing
pacbio
vecscreen
13 days ago by
Dunois
★ 2.5k
4
votes
7
replies
566
views
DESeq2 Multifactor Design
RNA-seq
DESeq2
updated 15 days ago by
Ram
43k • written 16 days ago by
AHerik
▴ 20
0
votes
0
replies
194
views
SeuratDisk: including "counts" dataset in conversion to AnnData
Seurat
SeuratDisk
AnnData
updated 16 days ago by
Ram
43k • written 16 days ago by
roussine
▴ 10
0
votes
0
replies
184
views
I am getting more annotation hits from HOMER than I have actual peaks. Is that normal?
ATAC-seq
HOMER
16 days ago by
Ronin
• 0
4
votes
13
replies
888
views
RNAseq of primary tumor and metastases in two different organ
metastases
RNA-seq
DEG
R
updated 12 days ago by
BioinfGuru
★ 1.7k • written 18 days ago by
matteo.levorato
• 0
2
votes
1
reply
251
views
VEP annotation --per_gene allele choice
VEP
updated 16 days ago by
Ram
43k • written 17 days ago by
atariw
▴ 10
0
votes
2
replies
293
views
Are GeneExpression Subtype annotations removed from TCGA-GBM?
tcga-gbm
subtyping
tcga
updated 16 days ago by
Zhenyu Zhang
★ 1.2k • written 17 days ago by
Apollonia
• 0
1
vote
1
reply
250
views
RNA seq normalization and gene gene correlation
rna-seq
pearson-correlation
vst
updated 16 days ago by
Ram
43k • written 17 days ago by
Fish
• 0
0
votes
0
replies
187
views
Snakemake fails to find conda in PBS
snakemake
17 days ago by
yixinzeng
• 0
0
votes
0
replies
189
views
KaryoPlot: Gene coverage over centromeric regions
Gene
coverage
Centromere
Bedtools
17 days ago by
Mary
• 0
0
votes
0
replies
182
views
Protein stability analysis
mutation
analysis
17 days ago by
marco.barr
▴ 80
1
vote
4
replies
399
views
what is the normal range of htseq-count output for homo sapiens RNA-Seq
Transcriptomics
htseq-count
RNA-Seq
NGS
hisat2
updated 16 days ago by
BioinfGuru
★ 1.7k • written 17 days ago by
Morteza
• 0
3
votes
1
reply
268
views
how to change the gene header names in a fasta file?
fasta
bioawk
awk
seqkit
updated 17 days ago by
Ram
43k • written 17 days ago by
rj.rezwan
• 0
0
votes
0
replies
172
views
Multiple Spike-Ins
MeRIP
Spike-In
17 days ago by
Adam
▴ 30
0
votes
0
replies
161
views
Tools for Sequence Consensus
Consensus-Sequence
bacteria
updated 17 days ago by
Ram
43k • written 17 days ago by
Reno
• 0
2
votes
2
replies
278
views
DepMap: siRNA and CRSIPR discrepancy
DepMap
updated 17 days ago by
ATpoint
82k • written 17 days ago by
Shicheng Guo
★ 9.4k
1
vote
0
replies
161
views
phasing tumor long-reads
nanopore
ONT
haplotag
phasing
tumor
17 days ago by
eesiribloom
▴ 80
0
votes
3
replies
326
views
10x GEX and ADT data analysis in Seurat
Seurat
scRNA-seq
ADT
Cite-seq
GEX
updated 16 days ago by
ATpoint
82k • written 17 days ago by
gdfsnkfns
• 0
0
votes
4
replies
326
views
Questions about transfering wgs file to reference genome file
fasta
cram
genome
17 days ago by
me
• 0
0
votes
2
replies
270
views
WGCNA
PCA
WGCNA
EIGENGENE
17 days ago by
rajasekargutha
▴ 60
0
votes
3
replies
272
views
BLASTP web- <20aa peptides- interpreting results/ minimum E value?
blast
peptide
blastp
alignment
updated 17 days ago by
GenoMax
141k • written 18 days ago by
neish
• 0
1
vote
0
replies
159
views
DESeq2 comparing timepoints within treatment and account for background control change
RNAseq
DEG
DESeq2
updated 17 days ago by
Ram
43k • written 18 days ago by
ian.will
▴ 30
0
votes
0
replies
108
views
Surrogate variable analysis for paired RNA seq experiment
sva
rnaseq
ruvseq
18 days ago by
nhaus
▴ 310
1
vote
3
replies
288
views
True variants selection
vcf
bcftools
updated 17 days ago by
dthorbur
★ 1.9k • written 18 days ago by
maevalefeuvre
• 0
0
votes
1
reply
168
views
How to reveal real AF of variant if duplicates can't be removed (such as in amplicon-seq)
allele-frequency
amplicon-seq
updated 17 days ago by
Ram
43k • written 18 days ago by
CY
▴ 750
0
votes
0
replies
111
views
Creating a BSgenome data package from a NCBI assembly - Virus
Virus
BSgenomeForge
BSgenome
R
18 days ago by
JirMan
▴ 20
1
vote
1
reply
177
views
Failed to download data from EBI with ascp
EBI
aspera
updated 18 days ago by
GenoMax
141k • written 18 days ago by
biock
▴ 60
0
votes
0
replies
400
views
BETA whether on the same scale when performing rank-based inverse normal transformation on the same type of phenotype data for two cohorts separately…
normal
inverse
transformation
18 days ago by
Isaac
• 0
0
votes
0
replies
109
views
Combining VG graphs
vg
graphs
combine
18 days ago by
AshleeThomson
▴ 80
0
votes
0
replies
116
views
Installing SALSA and HIRise scafolding software
scafolding
SALSA
genome-assembly
HIRise
updated 17 days ago by
Ram
43k • written 18 days ago by
Lissa Cruz Saavedra
• 0
0
votes
1
reply
186
views
Extract Di-nucleotide/Tri-Nucleotide substitution frequencies from MSA/VCF file
MSA
substitution
VCFstats
Evolution
VCF
updated 18 days ago by
Pierre Lindenbaum
161k • written 18 days ago by
Saran
▴ 50
0
votes
2
replies
276
views
Abundance Calculation in MetaPhlAn 3: Methodology, TPM or RPKM, and the Treatment of Unclassified Reads
MetaPhlAn
Normalization
RPKM
TPM
16 days ago by
ramin.k2013
• 0
0
votes
0
replies
163
views
Normalization in Metagenomics Sequencing By Total Number of Reads: Pre- or Post-Filtering and the Role of Unclassified Reads
Normalization
Metagenomics
updated 17 days ago by
Ram
43k • written 18 days ago by
ramin.k2013
• 0
0
votes
1
reply
177
views
Help with generating annotation database for dog genome to use in ANNOVAR for variant annotation of dog tumor sequences
ANNOVAR
updated 18 days ago by
Pierre Lindenbaum
161k • written 18 days ago by
sainavyav22
• 0
1,000 results • Page
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Recent Votes
Answer: High Malat-1 expression in single cell data
Answer: High Malat-1 expression in single cell data
The Biostar Herald for Monday, April 29, 2024
A: Bam And Indexed Bam Files
High Malat-1 expression in single cell data
Segmentation fault using gemma
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
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Recent Replies
Comment: High Malat-1 expression in single cell data
by
dsull
★ 5.9k
Malat1 is a lncRNA abundant in the nucleus. I guess if Malat1 is abundant and stable, makes sense it could be detect in high amounts in scR…
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• 0
Where can I ask this question? Apparently this the place where you can help for toil?
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Dear Gordon, excuse me for not being specific regarding your advice. What would be the best way if I wanted to add new annotations to the …
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141k
While you wait to get answers, consider asking ChatGPT for a solution. You may be pleasantly surprised with pointers/code you will get.
Comment: High Malat-1 expression in single cell data
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Kazo
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When I perform differential analysis, the genes that could be considered as markers in this malat1 high cluster tend to be nuclear genes. D…
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You can check where the application was installed using: https://unix.stackexchange.com/questions/39590/apt-get-install-where-does-it-go T…
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★ 5.9k
"using RNA-seq for allele imbalanced gene expression" -> Not sure what you mean by that; thousands of studies (including some ongoing studi…
Comment: High Malat-1 expression in single cell data
by
Kazo
▴ 10
I have noticed in articles that people define low-quality clusters and remove them from the data, but they don't exactly explain what makes…
Answer: High Malat-1 expression in single cell data
by
dsull
★ 5.9k
I'm assuming you read https://kb.10xgenomics.com/hc/en-us/articles/360004729092-Why-do-I-see-high-levels-of-Malat1-in-my-gene-expression-da…
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I actually advised you not to remove duplicate probes, especially as you seem to be use probe annotation that is very old and possibly out …
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by
dimpleadiwal050896
• 0
Hello, were you able to rectify this. If yes, do tell. I am getting a similar error. Thank you
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If the data is a technical sequencing replicate i.e. the same pool of samples has run on two lanes then you can indeed merge the two lanes …
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Galaxy specific requests are best posted on their help forum: https://help.galaxyproject.org/
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141k
You can simply `cat` all reference sequences together. Create an index file with `bowtie2` and then align as usual.
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