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13,516 results • Page
1 of 271
Sort: Rank
Rank
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Votes
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0
votes
2
replies
79
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
updated 1 hour ago by
Ram
43k • written 4 hours ago by
Ruqaiya
• 0
0
votes
0
replies
56
views
How to assign cell types after integration in scRNA
integration
conditions
ScRNA
seq
9 hours ago by
Francesco
▴ 10
0
votes
0
replies
59
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
9 hours ago by
tnminh89
▴ 10
7
votes
7
replies
454
views
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
2 hours ago by
noodle
▴ 520
795
votes
167
replies
142k
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
0
replies
60
views
Extract protein sequence
fasta
alighment
blast
10 hours ago by
anna
▴ 20
0
votes
0
replies
58
views
Filter low express genes in microarray data
microarray
11 hours ago by
Chris
▴ 260
0
votes
1
reply
250
views
absolute path for symbolic links in Snakefile
Snakemake
updated 12 hours ago by
Jesse
▴ 740 • written 8 days ago by
yifangt86
▴ 60
0
votes
2
replies
257
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment
gaps
updated 12 hours ago by
Jesse
▴ 740 • written 3 days ago by
Broccoli
• 0
2
votes
3
replies
240
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 13 hours ago by
Arup Ghosh
3.2k • written 1 day ago by
chaco001
▴ 40
0
votes
3
replies
225
views
Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:1.1.1.4, 1.1.1.-, 1.1.1.303)?
ontology
metagenomics
database
enzymes
genomics
updated 5 hours ago by
Mensur Dlakic
★ 27k • written 1 day ago by
O.rka
▴ 710
0
votes
1
reply
147
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
updated 1 day ago by
Gordon Smyth
★ 7.0k • written 1 day ago by
hagl
▴ 10
0
votes
2
replies
181
views
Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
RNA-Seq
edgeR
20 hours ago by
Guille
• 0
1
vote
1
reply
135
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
updated 1 day ago by
Gordon Smyth
★ 7.0k • written 1 day ago by
pairedttest
▴ 10
3
votes
6
replies
1.9k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 1 day ago by
Ram
43k • written 2.4 years ago by
SYOSY
▴ 10
0
votes
0
replies
303
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
1 day ago by
biocellbio
• 0
4
votes
8
replies
513
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 1 day ago by
Alex Reynolds
35k • written 2 days ago by
J
▴ 10
4
votes
7
replies
572
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 1 day ago by
dsull
★ 5.9k • written 5 days ago by
qudrat.nii
▴ 10
0
votes
0
replies
102
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 1 day ago by
Ram
43k • written 1 day ago by
vanbelj
▴ 40
19
votes
11
replies
14k
views
10 follow
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
utr
updated 1 day ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
2
votes
2
replies
246
views
what is the purpose of indexing the reference genome (Kallisto)
indexing
Kallisto
updated 1 day ago by
dsull
★ 5.9k • written 2 days ago by
Aaliya
▴ 10
3
votes
0
replies
142
views
News:
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy
Generative-AI
scRNA
Machine-Learning
updated 1 day ago by
Ram
43k • written 1 day ago by
Claire Watson
▴ 60
0
votes
2
replies
211
views
Rare Disease Variant Pathway Analysis
Pathway-analysis
updated 1 day ago by
Ram
43k • written 2 days ago by
The_PyPanda
▴ 10
0
votes
0
replies
146
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
1 day ago by
HarperReed
• 0
3
votes
3
replies
216
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 1 day ago by
GenoMax
141k • written 1 day ago by
sapuizait
▴ 10
1
vote
0
replies
109
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
2 days ago by
KABILAN
▴ 50
0
votes
0
replies
118
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 1 day ago by
Ram
43k • written 2 days ago by
SineWave
• 0
0
votes
0
replies
113
views
RNA-seq: full length gene
RNA-seq
updated 1 day ago by
Ram
43k • written 2 days ago by
Nargis
• 0
1
vote
6
replies
282
views
gvcf joint calling
WES
GATK
VCF
gVCF
updated 3 hours ago by
Jeremy Leipzig
22k • written 2 days ago by
zihanss
• 0
0
votes
0
replies
107
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
2 days ago by
turcoa1
• 0
3
votes
3
replies
236
views
Sequence read length shorter than flow cell specification
illumina
NGS
sequencing
updated 2 days ago by
swbarnes2
14k • written 2 days ago by
M
• 0
0
votes
0
replies
118
views
Designing single-stable RNA molecules
structure
RNA
2 days ago by
Edna
• 0
0
votes
0
replies
132
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
2 days ago by
simplitia
▴ 130
0
votes
1
reply
169
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 2 days ago by
ATpoint
82k • written 2 days ago by
AaronJaime
• 0
0
votes
2
replies
229
views
BLAST using both nucleotides and taxonomic local databases
blast
ncbi
taxid
taxonomy
updated 2 days ago by
GenoMax
141k • written 2 days ago by
Begonia_pavonina
▴ 150
0
votes
2
replies
260
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
updated 2 days ago by
Ram
43k • written 2 days ago by
Assa Yeroslaviz
★ 1.8k
1
vote
2
replies
247
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell-markers
9 hours ago by
Francesco
▴ 10
1
vote
6
replies
362
views
ScRNA data question
scRNA
Vlnplot
Samples
19 hours ago by
starswillfade
▴ 10
0
votes
0
replies
134
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
2 days ago by
avocado123
• 0
0
votes
0
replies
125
views
News:
Master Meta-analysis with R (May 13-16) - Online!
Meta-Analysis
Statistics
R
updated 2 days ago by
Ram
43k • written 2 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
123
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
2 days ago by
Emily
▴ 10
1
vote
0
replies
142
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
2 days ago by
rohitsatyam102
▴ 850
0
votes
0
replies
125
views
how to read graph_test output of monocle 3
monocle3
2 days ago by
synat.keam
▴ 100
0
votes
0
replies
155
views
Job:
CTO/founding engineer role at Voyant Bio
engineer
2 days ago by
Assaf
• 0
0
votes
1
reply
453
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 2 days ago by
ginellegrenier
• 0 • written 4 months ago by
Clayton
• 0
3
votes
4
replies
295
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
2 days ago by
QX
• 0
2
votes
1
reply
211
views
Finding orthologs between genome error
OMA
OMAbrowser
updated 2 days ago by
Adrian Altenhoff
★ 1.1k • written 3 days ago by
hemantcnaik
• 0
0
votes
0
replies
136
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
2 days ago by
Aspire
▴ 300
2
votes
4
replies
306
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
updated 2 days ago by
Ram
43k • written 3 days ago by
ashaneev07
▴ 20
2
votes
3
replies
250
views
Figures are disappeared from html report of SnpEff
HTML
SnpEff
updated 2 days ago by
Pierre Lindenbaum
161k • written 2 days ago by
analyst
▴ 30
13,516 results • Page
1 of 271
Recent Votes
Comment: NGS forensics: how to know if data is fabricated
Comment: calculate nucleotide diversity from whole-genome-sequence data for individual ge
Comment: calculate nucleotide diversity from whole-genome-sequence data for individual ge
Answer: DNA methylation preprocessing
Comment: NGS forensics: how to know if data is fabricated
Answer: NGS forensics: how to know if data is fabricated
Comment: NGS forensics: how to know if data is fabricated
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Recent Replies
Answer: How many reads for WGS Sequencing?
by
Mensur Dlakic
★ 27k
It takes 29 seconds to assemble this genome (20 CPUs) with the following statistics: 135 contigs, total 2821177 bp, min 200 bp, max …
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 520
IMO (and unfortunately) there needs to be an effort to develop these algorithms.
Comment: gvcf joint calling
by
Jeremy Leipzig
22k
the samples that are `./.` have no coverage (or not enough to call a genotype) and the `0/0` are homozygous reference
Answer: How many reads for WGS Sequencing?
by
GenoMax
141k
Did you download the complete dataset available from ENA/NCBI SRA? This is an older dataset (from 2012) with a total of 1146212 reads and 1…
Comment: When to use .vcf or .gvcf files from GATK HaplotypeCaller?
by
zihanss
• 0
Hello, I want to know that why my gVCF files have "./." besides "0/0", "1/1"? Thanks
Comment: gvcf joint calling
by
zihanss
• 0
![enter image description here][1] [1]: /media/images/15eedc1a-b2c6-4966-be39-b5173dab And I confused with the file that has "./." and…
Comment: gvcf joint calling
by
zihanss
• 0
![enter image description here][1] [1]: /media/images/16fd502c-4e01-4f56-8562-0e0d4aac Okay, this is the merged gVCF file.
Comment: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
by
Mensur Dlakic
★ 27k
Enzymes under the umbrella of `1.1.1.-` work `with NAD(+) or NADP(+) as acceptor`. That only tells you about their cofactors, but not about…
Comment: NGS forensics: how to know if data is fabricated
by
dsull
★ 5.9k
I don't think people have undertaken the effort to create an anomaly detector for RNAseq -- people's efforts are dedicated towards developi…
Comment: NGS forensics: how to know if data is fabricated
by
dsull
★ 5.9k
I'd say post on pubpeer -- it's the best forum for this sort of discussion. As for what additional analysis I recommend: I'd say look at s…
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 520
> This is a super-interesting question from an algorithmic standpoint Ya, I was hoping to find some algorithm that would compare say a 're…
Comment: ScRNAseq-How to correctly choose cell type marker genes
by
Francesco
▴ 10
Thank you for your valuable suggestion!
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 520
> My first question would be how strong your background in such analysis > is. Very strong. PhD+several years working in the field. > Wot…
Comment: NGS forensics: how to know if data is fabricated
by
ATpoint
82k
My first question would be how strong your background in such analysis is. Claim of fabrication is very serious, so be 100% sure to back it…
Answer: NGS forensics: how to know if data is fabricated
by
Jeremy Leipzig
22k
This is a super-interesting question from an algorithmic standpoint (devising a model that can distinguish real from synthetic reads) but I…
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