Limit : this week
all time today this week this month this year
109 results • Page 2 of 3
Sort: Rank
Rank Views Votes Replies
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
2
votes
4
replies
248
views
interpretartion of a vcf file
calling genotype ONT variant diploid
1 day ago by samuelkalandarov2002 ▴ 10
0
votes
0
replies
78
views
Annotating single cell data automatically
cell annotation single
3 days ago by Gerard • 0
0
votes
1
reply
144
views
RNA-seq bacteria contamination
RNA-seq
updated 3 days ago by 141k • written 3 days ago by • 0
0
votes
0
replies
70
views
Imputation advice
imputation
3 days ago by kl ▴ 10
0
votes
0
replies
86
views
Trimming best practices for SNP calling
trimming SNP trimmomatic
3 days ago by Enrique • 0
0
votes
0
replies
71
views
Correct way of reducing predictive model complexity
lasso glmnet predictvemodeling regression
3 days ago by sativus ▴ 20
0
votes
0
replies
78
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER MARINA ARACNe
3 days ago by Biostars2200 • 0
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 8.7k • written 3 days ago by • 0
2
votes
5
replies
439
views
Marking duplicates using UMIs
Deduplication UMI
updated 3 days ago by 19k • written 4 days ago by • 0
0
votes
0
replies
138
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 4 days ago by 43k • written 4 days ago by • 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
132
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation CGenFF Gromacs VMD
4 days ago by Mamatha Y S • 0
0
votes
2
replies
257
views
bam merging for archaic samples
samtools bam
updated 4 days ago by 43k • written 5 days ago by ▴ 100
1
vote
0
replies
538
views
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers TRINITY
5 days ago by mathavanbioinfo ▴ 90
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
2
votes
5
replies
681
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 4 days ago by ▴ 740 • written 5 days ago by ★ 2.4k
0
votes
0
replies
186
views
agilent microarray gpl data does not have gene symbol column
microarray agilent gpl
updated 5 days ago by 43k • written 6 days ago by • 0
0
votes
0
replies
187
views
scRNA Cluster frequency
CV PCA scRNA Cluster-Frequency
6 days ago by Nitin • 0
0
votes
0
replies
187
views
absolute path for symbolic links in Snakefile
Snakemake
updated 6 days ago by 43k • written 6 days ago by ▴ 60
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 141k • written 6 days ago by ▴ 10
0
votes
0
replies
203
views
Copy number variation plot
Copy-number-variation genomics
updated 6 days ago by 43k • written 6 days ago by • 0
0
votes
0
replies
177
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs ngsTools ANGSD genomics
6 days ago by DanielEB_fisk ▴ 20
0
votes
1
reply
280
views
Could you please assist in identifying this cluster?
single-cell
updated 6 days ago by 43k • written 6 days ago by • 0
0
votes
0
replies
194
views
Conversion to tree format
PLINK bed Figtree SplitsTree
updated 6 days ago by 43k • written 6 days ago by • 0
0
votes
0
replies
193
views
miRDeep2: How to get the read counts
mirdeep2
6 days ago by Atul K. • 0
0
votes
0
replies
201
views
Lncipedia GTF file error
Proteomics
updated 6 days ago by 43k • written 6 days ago by ▴ 10
3
votes
3
replies
466
views
Free/open source 23andme-like analysis
SNPs genomics NGS VCF
updated 5 days ago by 14k • written 6 days ago by ▴ 510
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
0
replies
213
views
create genewise sync file in popoolation
popoolation
updated 6 days ago by 141k • written 6 days ago by • 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
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
0
replies
202
views
traying to make a maf from an already annotated vcf
vcf vcf2maf maf maftools VEP
3 days ago by Javier • 0
1
vote
1
reply
412
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA Limma
updated 4 days ago by ★ 7.0k • written 7 days ago by ▴ 260
1
vote
1
reply
393
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow python-apollo Apollo
6 days ago by renan.igor • 0
0
votes
4
replies
574
views
Per base sequence content failed miserably
fastqc sequence trimmomatic NGS assembly
6 days ago by Kai Xin • 0
2
votes
7
replies
811
views
Removing duplicates
duplicates ONT minimap2
updated 6 days ago by ▴ 510 • written 8 days ago by • 0
1
vote
2
replies
228
views
permutation test in edgeR
rna-seq edgeR
updated 3 days ago by ★ 7.0k • written 17 days ago by • 0
0
votes
6
replies
424
views
Use of Kraken output for functional analysis
metagenomics kraken shotgun
updated 1 day ago by • 0 • written 24 days ago by ▴ 20
0
votes
2
replies
537
views
autodockvina
python python3 autodock
updated 6 days ago by 43k • written 4 months ago by • 0
0
votes
0
replies
273
views
Choice of relatedness cutoff for GWAS of a large cohort (>100K samples)
relatedness IBD GWAS
updated 2 days ago by 43k • written 14 months ago by ▴ 10
2
votes
4
replies
1.4k
views
How to fix Error in dat[, batch == batch_level] : (subscript) logical subscript too long when removing batch effects
microarray combat batch-effect median-normalization
updated 6 days ago by 43k • written 18 months ago by • 0
0
votes
0
replies
732
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
RNA-Seq scRNA-Seq batch-effect
updated 6 days ago by 43k • written 3.4 years ago by ▴ 180
0
votes
1
reply
818
views
Bulk RNAseq MACS Sort Quality Contamination
EdgeR Batch-effect RNA-Seq
updated 6 days ago by 43k • written 3.7 years ago by • 0
0
votes
0
replies
1.2k
views
Batch estimate using kBET
batch-effect kbet
updated 6 days ago by 43k • written 4.0 years ago by • 0
0
votes
0
replies
1.8k
views
Differential expression using Scran batch corrected data
single-cell Batch-effect RNA-Seq Scran
updated 6 days ago by 43k • written 5.5 years ago by ▴ 10
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 • 0 • written 6.5 years ago by ▴ 30
1
vote
2
replies
1.9k
views
Remove batch effect from exome data
NGS exome-sequencing batch-effect
updated 6 days ago by 43k • written 6.5 years ago by ▴ 270
109 results • Page 2 of 3
Recent Votes
Answer: How do I get the 3bp sequence on either side of a co-ordinate
What is the difference between HaplotypeCaller and UnifiedGenotyper?
What is the difference between HaplotypeCaller and UnifiedGenotyper?
RSeQC Output from infer_experiment.py - what does it mean?
ScRNAseq-How to correctly choose cell type marker genes
ScRNA data question
Comment: SRA to BAM
Recent Locations • All
Bologna, just now
Karachi, just now
United States, 1 minute ago
Canada, 2 minutes ago
Finland, 2 minutes ago
São Paulo, 2 minutes ago
United States, 3 minutes ago
Recent Awards • All
Student to John Torcivia ▴ 70
Popular Question to bioinfo ▴ 150
Popular Question to jvijai ★ 1.2k
Scholar to otieno43 ▴ 30
Supporter to DBScan ▴ 300
Popular Question to Begonia_pavonina ▴ 150
Popular Question to BCArg ▴ 90
Recent Replies
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 ▴ 840
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 …
Comment: GAPIT p-value significance threshold by ginellegrenier • 0
Hi, I was wondering if you have found a solution to this? Thanks!
Comment: PCA plot by jkim ▴ 170
cross posted in bioconductor. [https://support.bioconductor.org/p/9157968/][1] [1]: https://support.bioconductor.org/p/9157968/
Comment: ScRNA data question by bk11 ★ 2.3k
Which normalization method did you use for your data? I am guessing you had used SCTransform normalization for your data. Can you plot usin…
Comment: How to make a TSS enrichment plot in ATAC-seq analysis? by sp • 0
Hi Dan, I was wondering if you found out how to make the same graph with NFR and NBR regions with different curves. I was able to recreate…
Comment: Why gatk VariantAnnotator required bam and coverage files by QX • 0
I think the coverage could also computed from bam file itself, but let say I do not include the coverage, do you have any idea why it needs…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas by GenoMax 141k
I am moving my answer to a comment. At this point you should email NCBI help desk and ask them this question. If you get an answer then ple…
Comment: Figures are disappeared from html report of SnpEff by Pierre Lindenbaum 161k
the javascript in your html is deprecated or your firefox is just tool old.
Comment: Why gatk VariantAnnotator required bam and coverage files by Pierre Lindenbaum 161k
> I would like to ask why they may require the bam file for this function? hum.. if you want to add the coverage, where do you think gatk …
Traffic: 2898 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6