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116,610 results • Page
1 of 2333
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Designing single-stable RNA molecules
structure
RNA
just now by
Anna
• 0
0
votes
0
replies
12
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
just now by
simplitia
▴ 130
0
votes
1
reply
32
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 1 hour ago by
ATpoint
82k • written 1 hour ago by
AaronJaime
• 0
0
votes
2
replies
99
views
BLAST using both nucleotides and taxonomic local databases
blast
ncbi
taxid
taxonomy
updated 2 hours ago by
GenoMax
141k • written 9 hours ago by
Begonia_pavonina
▴ 150
795
votes
167
replies
141k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.7k • written 7.4 years ago by
Istvan Albert
100k
0
votes
2
replies
140
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
updated 3 hours ago by
Bioinfotec
▴ 10 • written 11 hours ago by
Assa Yeroslaviz
★ 1.8k
1
vote
1
reply
88
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell-markers
updated 44 minutes ago by
Ram
43k • written 7 hours ago by
Francesco
▴ 10
1
vote
2
replies
110
views
ScRNA data question
scRNA
Vlnplot
Samples
updated 3 hours ago by
Bioinfotec
▴ 10 • written 7 hours ago by
starswillfade
▴ 10
0
votes
0
replies
39
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
4 hours ago by
avocado123
• 0
0
votes
0
replies
36
views
News:
Master Meta-analysis with R (May 13-16) - Online!
Meta-Analysis
Statistics
R
updated 46 minutes ago by
Ram
43k • written 4 hours ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
36
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
4 hours ago by
Emily
▴ 10
1
vote
0
replies
42
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
4 hours ago by
rohitsatyam102
▴ 850
2
votes
2
replies
79
views
Sequence read length shorter than flow cell specification
illumina
NGS
sequencing
updated 4 hours ago by
GenoMax
141k • written 5 hours ago by
M
• 0
0
votes
0
replies
38
views
how to read graph_test output of monocle 3
monocle3
5 hours ago by
synat.keam
▴ 100
0
votes
0
replies
49
views
Job:
CTO/founding engineer role at Voyant Bio
engineer
5 hours ago by
Assaf
• 0
0
votes
1
reply
372
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 6 hours ago by
ginellegrenier
• 0 • written 4 months ago by
Clayton
• 0
3
votes
4
replies
156
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
1 hour ago by
QX
• 0
2
votes
1
reply
129
views
Finding orthologs between genome error
OMA
OMAbrowser
updated 11 hours ago by
Adrian Altenhoff
★ 1.1k • written 1 day ago by
hemantcnaik
• 0
0
votes
0
replies
56
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
12 hours ago by
Aspire
▴ 300
2
votes
4
replies
202
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
updated 40 minutes ago by
Ram
43k • written 15 hours ago by
ashaneev07
▴ 20
2
votes
3
replies
163
views
Figures are disappeared from html report of SnpEff
HTML
SnpEff
updated 9 hours ago by
Pierre Lindenbaum
161k • written 13 hours ago by
analyst
▴ 30
0
votes
1
reply
107
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment
gaps
updated 13 hours ago by
b.contreras.moreira
▴ 170 • written 14 hours ago by
Broccoli
• 0
0
votes
2
replies
136
views
Highest variable features in single cell data
single-cell
updated 40 minutes ago by
Ram
43k • written 14 hours ago by
Kazo
• 0
0
votes
1
reply
138
views
Network Alignment
plugin
Cytoscape
CytoMCS
updated 16 hours ago by
Scooter
▴ 280 • written 1 day ago by
Akash D
▴ 40
2
votes
4
replies
2.3k
views
How could I generate a gi_taxid_nucl.dmp file similar to the one previously hosted by NCBI?
ncbi
metagenomics
centrifuge
gi_taxid_nucl.dmp
taxonomy
updated 17 hours ago by
ZhangYuanfeng
• 0 • written 2.4 years ago by
Frazier Baker
• 0
0
votes
1
reply
124
views
PCA plot
DESeq2
PCAplot
updated 6 hours ago by
jkim
▴ 170 • written 17 hours ago by
Aaliya
▴ 10
0
votes
1
reply
87
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 34 minutes ago by
Ram
43k • written 17 hours ago by
Ming Tommy Tang
★ 3.9k
0
votes
3
replies
267
views
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 40 minutes ago by
Ram
43k • written 2 days ago by
qudrat.nii
▴ 10
0
votes
4
replies
2.6k
views
Lositan freezing when generating selection table
LOSITAN
updated 19 hours ago by
evawillms183
• 0 • written 8.3 years ago by
andrepleao
• 0
0
votes
0
replies
82
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
20 hours ago by
4fzcgueyp5
• 0
2
votes
3
replies
259
views
clustalo - align milions of short seq, memory issue
memory
clustalo
updated 3 days ago by
Mensur Dlakic
★ 27k • written 3 days ago by
emmanouil.a
▴ 120
0
votes
2
replies
148
views
Annovar using R package
Annovar
gnomAD
R
39 minutes ago by
DKA
▴ 40
0
votes
2
replies
167
views
Creating Synthetic Sequences for a ML Model
DNA
ML
updated 23 hours ago by
Mensur Dlakic
★ 27k • written 1 day ago by
biochugs
• 0
3
votes
8
replies
462
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 15 hours ago by
swbarnes2
14k • written 1 day ago by
Aaliya
▴ 10
1
vote
8
replies
734
views
Adding CB tag to bam file
samtools
bam
updated 13 hours ago by
Pierre Lindenbaum
161k • written 6 days ago by
Maria
• 0
1
vote
10
replies
884
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
1 day ago by
DKA
▴ 40
0
votes
2
replies
769
views
AGeNT LocatIt
AGeNT
LocatIt
WES
UMI
duplicates
updated 1 day ago by
barslmn
★ 2.1k • written 2.8 years ago by
jhy
▴ 10
0
votes
5
replies
260
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 7 hours ago by
GenoMax
141k • written 1 day ago by
Bertalan_Takacs
▴ 90
0
votes
0
replies
109
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 1 day ago by
Ram
43k • written 1 day ago by
glaciya2018
• 0
0
votes
0
replies
91
views
News:
8th Berlin Summer School in NGS Data Analysis - Apply Now
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
updated 40 minutes ago by
Ram
43k • written 1 day ago by
David Langenberger
11k
0
votes
0
replies
203
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
13
replies
3.5k
views
6 follow
Tax4Fun2 - error
tax4fun
silva
blast
updated 1 day ago by
drstalinantony28
• 0 • written 2.2 years ago by
ymj
▴ 10
0
votes
1
reply
126
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
113
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
1 day ago by
salias
• 0
4
votes
7
replies
385
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 12 hours ago by
dsull
★ 5.8k • written 1 day ago by
VITALA
• 0
0
votes
4
replies
235
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
12 hours ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
99
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 1 day ago by
Ram
43k • written 1 day ago by
newuser2024
• 0
1
vote
2
replies
180
views
alignment result
RNA-seq
samtools
hisat2
15 hours ago by
ahmad.sajad4541
• 0
0
votes
0
replies
97
views
News:
hands-on introduction to generalized linear models (GLMs) using R
Generalized-Linear-Models
GLM
R
updated 1 day ago by
Ram
43k • written 1 day ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
90
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
DoubletFinder
Seurat
modelHomotypic
updated 1 day ago by
Ram
43k • written 1 day ago by
Jeyong
• 0
116,610 results • Page
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Recent Votes
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
Detecting somatic variants in non-tumor tissue without normals
Answer: Sequence read length shorter than flow cell specification
Answer: Sequence read length shorter than flow cell specification
Comment: Why gatk VariantAnnotator required bam and coverage files
A: Generate Vcf.Gz File And Its Index File Vcf.Gz.Tbi
Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
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Recent Replies
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
Ram
43k
Thank you, the `csvtk spread` is super useful. I usually import into R using `lapply` then `Reduce` using `merge` but this might be easier.
Comment: Annovar using R package
by
DKA
▴ 40
Thank you for your guidance. The thing is that I am unfamiliar with using such environments, unfortunately.
Comment: Treatment VS Control in Single Cell RNAseq analysis
by
ATpoint
82k
Open a new question, with details.
Comment: Normalize scRNAseq data to housekeeping genes to compare several datasets
by
ATpoint
82k
I recommend https://bioconductor.org/books/3.18/OSCA.basic/normalization.html as well as the "advanced" section in this book.
Comment: Why gatk VariantAnnotator required bam and coverage files
by
QX
• 0
thank you!
Comment: Treatment VS Control in Single Cell RNAseq analysis
by
kilcdincer
▴ 10
Hello, I have more or less same experimental setting and was wondering how you proceeded with your analysis? Can I reach its GitHub reposit…
Comment: BLAST using both nucleotides and taxonomic local databases
by
GenoMax
141k
> I ask this as some BLAST command fields as scinames or sblastnames do not give any output with a classic nt BLAST If that information is…
Answer: BLAST using both nucleotides and taxonomic local databases
by
5heikki
11k
This has been discussed [many times][1] [1]: https://www.biostars.org/p/76551/
Answer: why renaming Idents in Seurat object doesn't work?
by
Bioinfotec
▴ 10
I think when you give indent to seuObj : Idents(seuObj) <- 'RNA_snn_res.0.1' You may wrongly assign other value to it such as …
Answer: ScRNAseq-How to correctly choose cell type marker genes
by
Bioinfotec
▴ 10
In fact, there is no gold standard for cell type annotation. To achieve correct cell type classification, you can combine the two methos. F…
Answer: ScRNA data question
by
Bioinfotec
▴ 10
In violin plot, a dot represents a cell. Actually, the straight lines you see in your infected image just means these cells have the same e…
Comment: Sequence read length shorter than flow cell specification
by
GenoMax
141k
> the have sent data with different sequencing read lengths: 55bp pair ended and 80bp single ended If they sent data that is not what you…
Comment: How to know synonymous and non-synonymous SNPs from transcriptome sequencing
by
rohitsatyam102
▴ 850
I have some off-the-chart dN/dS values for few genes (>20) when using your script on VCF obtained from a 20K plasmodium genomes (pf7K). | …
Answer: Sequence read length shorter than flow cell specification
by
ATpoint
82k
It is the amount of reagent in the kit that determines read length. Sometimes index cycle reagents are allocated to R1/R2 or they used anot…
Comment: Why gatk VariantAnnotator required bam and coverage files
by
Pierre Lindenbaum
161k
you don't need the bam file https://gatk.broadinstitute.org/hc/en-us/articles/13832654601755-VariantAnnotator : VariantAnnotator …
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