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195 results • Page
3 of 4
Sort: Votes
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0
votes
2
replies
107
views
BLAST using both nucleotides and taxonomic local databases
blast
ncbi
taxid
taxonomy
updated 3 hours ago by
GenoMax
141k • written 10 hours ago by
Begonia_pavonina
▴ 150
0
votes
1
reply
47
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 2 hours ago by
ATpoint
82k • written 2 hours ago by
AaronJaime
• 0
0
votes
0
replies
39
views
News:
Master Meta-analysis with R (May 13-16) - Online!
Meta-Analysis
Statistics
R
updated 1 hour ago by
Ram
43k • written 5 hours ago by
carlopecoraro2
★ 2.5k
0
votes
2
replies
140
views
Highest variable features in single cell data
single-cell
updated 1 hour ago by
Ram
43k • written 15 hours ago by
Kazo
• 0
0
votes
3
replies
271
views
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 1 hour ago by
Ram
43k • written 2 days ago by
qudrat.nii
▴ 10
0
votes
2
replies
152
views
Annovar using R package
Annovar
gnomAD
R
1 hour ago by
DKA
▴ 40
0
votes
1
reply
96
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 1 hour ago by
Ram
43k • written 19 hours ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
93
views
News:
8th Berlin Summer School in NGS Data Analysis - Apply Now
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
updated 1 hour ago by
Ram
43k • written 1 day ago by
David Langenberger
11k
0
votes
0
replies
17
views
Designing single-stable RNA molecules
structure
RNA
1 hour ago by
Edna
• 0
0
votes
0
replies
22
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
1 hour ago by
simplitia
▴ 130
0
votes
2
replies
148
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
updated 16 minutes ago by
Ram
43k • written 12 hours ago by
Assa Yeroslaviz
★ 1.8k
0
votes
0
replies
5
views
Rare Disease Variant Pathway Analysis
Pathway
analysis
8 minutes ago by
The_PyPanda
▴ 10
0
votes
2
replies
533
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
6 days ago by
航太郎
• 0
0
votes
2
replies
372
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
6 days ago by
Ashok
• 0
0
votes
2
replies
410
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
6 days ago by
Ashok
• 0
0
votes
4
replies
575
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
6 days ago by
Kai Xin
• 0
0
votes
0
replies
194
views
miRDeep2: How to get the read counts
mirdeep2
6 days ago by
Atul K.
• 0
0
votes
0
replies
178
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs
ngsTools
ANGSD
genomics
6 days ago by
DanielEB_fisk
▴ 20
0
votes
2
replies
420
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
6 days ago by
_quantum_girl_
▴ 10
0
votes
1
reply
281
views
Could you please assist in identifying this cluster?
single-cell
updated 6 days ago by
Ram
43k • written 6 days ago by
Kazo
• 0
0
votes
0
replies
195
views
Conversion to tree format
PLINK
bed
Figtree
SplitsTree
updated 6 days ago by
Ram
43k • written 6 days ago by
Dinmukhamed
• 0
0
votes
0
replies
201
views
Lncipedia GTF file error
Proteomics
updated 6 days ago by
Ram
43k • written 6 days ago by
atharvakarkare14
▴ 10
0
votes
0
replies
203
views
Copy number variation plot
Copy-number-variation
genomics
updated 6 days ago by
Ram
43k • written 6 days ago by
Emmi
• 0
0
votes
0
replies
180
views
Chemical structure validation
structure
cap
validation
metabolite
6 days ago by
Rodolfo Adrián
• 0
0
votes
1
reply
259
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 6 days ago by
GenoMax
141k • written 6 days ago by
bioyas
▴ 10
0
votes
0
replies
187
views
absolute path for symbolic links in Snakefile
Snakemake
updated 6 days ago by
Ram
43k • written 6 days ago by
yifangt86
▴ 60
0
votes
0
replies
187
views
scRNA Cluster frequency
CV
PCA
scRNA
Cluster-Frequency
6 days ago by
Nitin
• 0
0
votes
0
replies
186
views
agilent microarray gpl data does not have gene symbol column
microarray
agilent
gpl
updated 6 days ago by
Ram
43k • written 6 days ago by
mja
• 0
0
votes
5
replies
5.9k
views
Calculate Radius of Gyration [python 3]
biopython
PDB
Radius of Gyration
python
protein
updated 5 days ago by
ndm1096
• 0 • written 6.5 years ago by
ac.research
▴ 30
0
votes
0
replies
211
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
5 days ago by
abhishekghadge
• 0
0
votes
4
replies
518
views
how to find genes that are significantly expressed in brain cortex samples
rna-seq
gene-expression
updated 5 days ago by
ATpoint
82k • written 6 days ago by
rheab1230
▴ 140
0
votes
0
replies
133
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation
CGenFF
Gromacs
VMD
5 days ago by
Mamatha Y S
• 0
0
votes
0
replies
138
views
Bacterial genome alignment with mauve
Bacteria
mauve
genome
4 days ago by
rthapa
▴ 90
0
votes
0
replies
138
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 4 days ago by
Ram
43k • written 4 days ago by
sainavyav22
• 0
0
votes
0
replies
129
views
News:
upcoming online statistical courses
Statistics
R
Data-Analysis
updated 4 days ago by
Ram
43k • written 5 days ago by
carlopecoraro2
★ 2.5k
0
votes
2
replies
258
views
bam merging for archaic samples
samtools
bam
updated 4 days ago by
Ram
43k • written 5 days ago by
Matteo Ungaro
▴ 100
0
votes
0
replies
125
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 3 days ago by
Carlo Yague
8.7k • written 3 days ago by
Atul K.
• 0
0
votes
1
reply
174
views
homology modelling using swiss model
homology-modeling
swiss-model
updated 3 days ago by
colindaven
6.4k • written 4 days ago by
Ayush
• 0
0
votes
0
replies
79
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER
MARINA
ARACNe
3 days ago by
Biostars2200
• 0
0
votes
0
replies
72
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
3 days ago by
sativus
▴ 20
0
votes
0
replies
89
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
3 days ago by
Enrique
• 0
0
votes
0
replies
70
views
Imputation advice
imputation
3 days ago by
kl
▴ 10
0
votes
1
reply
128
views
FAM FILE
file
Fam
3 days ago by
Eleonora
• 0
0
votes
0
replies
187
views
Job:
Ensembl Outreach Project Leader
ebi
embl
genomics
ensembl
3 days ago by
Ben_Ensembl
★ 2.4k
0
votes
0
replies
121
views
Job:
Ensembl Plants Senior Bioinformatician
ebi
embl
genomics
ensembl
3 days ago by
Ben_Ensembl
★ 2.4k
0
votes
0
replies
80
views
News:
Online course: DNA methylation
Pacbio
Nanopore
DnaMethylation
Evolution
3 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
79
views
Annotating single cell data automatically
cell
annotation
single
3 days ago by
Gerard
• 0
0
votes
0
replies
80
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
3 days ago by
feather-W
• 0
0
votes
2
replies
187
views
Result of running of p3_in.pl
primer3
updated 3 days ago by
GenoMax
141k • written 3 days ago by
nasri
• 0
0
votes
1
reply
147
views
RNA-seq bacteria contamination
RNA-seq
updated 3 days ago by
GenoMax
141k • written 3 days ago by
sh
• 0
195 results • Page
3 of 4
Recent Votes
Comment: Sequence read length shorter than flow cell specification
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
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Scholar
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ATpoint
82k
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zdiazmar
▴ 30
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Recent Replies
Answer: Sequence read length shorter than flow cell specification
by
swbarnes2
14k
The company probably had you share your run with someone who needed the extra bases. So you get the extra bases free. Just use them unle…
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 : ```r 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…
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