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484 results • Page
4 of 10
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Votes
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0
votes
2
replies
61
views
PDB related issue
rcsb
pdb
updated 38 minutes ago by
noodle
▴ 530 • written 3 hours ago by
Nafi
• 0
0
votes
1
reply
161
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 5 days ago by
bk11
★ 2.4k • written 5 days ago by
alphaflylizard
• 0
0
votes
0
replies
168
views
Analyzing differentially methylated regions from Nanopore long read data?
Long-read-sequencing
methylation
updated 23 days ago by
Ram
43k • written 6 weeks ago by
Arton
• 0
0
votes
0
replies
623
views
I performed Homer's annotatePeaks.pl on multiple tissues, yet when I run annotatePeaks on the merged tissues, I get fewer total annotated peaks. Is t…
Homer
ATACseq
29 days ago by
Ronin
• 0
0
votes
2
replies
252
views
Problem with downloading genome in SnpEff
SnpEff
18 days ago by
Javier
• 0
0
votes
0
replies
97
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 5 days ago by
Ram
43k • written 6 days ago by
Amélie
• 0
0
votes
0
replies
399
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
17 days ago by
Isaac
• 0
0
votes
0
replies
326
views
Finding the number of CpG sites in rainbow trout reference genome
reference-genome
CpG
updated 26 days ago by
Ram
43k • written 2.3 years ago by
marina.el-kamouh
• 0
0
votes
0
replies
107
views
Databases with GoF (Gain of Function) annotations.
gof
lof
gain-of-function
19 days ago by
_quantum_girl_
▴ 10
0
votes
2
replies
625
views
Seeking Alternative Tools for Predicting Mature microRNAs from Vertebrate Animal Precursors in In Silico Study
mirdeep2
maturebayes
microrna
updated 26 days ago by
Ram
43k • written 12 months ago by
Beatriz
• 0
0
votes
0
replies
98
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
5 days ago by
ohtang7
▴ 40
0
votes
2
replies
381
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
9 days ago by
Ashok
• 0
0
votes
1
reply
456
views
principal coordinate analysis
PCoA
R
updated 26 days ago by
Ram
43k • written 10 months ago by
rene.j.erhardt
▴ 20
0
votes
0
replies
128
views
How to annotate pairwise p value from limma (3 groups) in a combine multiple boxplot?
limma
boxplot
19 days ago by
Chris
▴ 260
0
votes
0
replies
183
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
0
votes
0
replies
190
views
scRNA Cluster frequency
CV
PCA
scRNA
Cluster-Frequency
9 days ago by
Nitin
• 0
0
votes
0
replies
105
views
How to extract BED-format annotation tracks for the newly inserted segments
bed
mauve
updated 26 days ago by
Ram
43k • written 26 days ago by
FZ
• 0
0
votes
0
replies
208
views
Copy number variation plot
Copy-number-variation
genomics
updated 9 days ago by
Ram
43k • written 9 days ago by
Emmi
• 0
0
votes
2
replies
226
views
How to detect and visualize ORFs in bacterial genome?
statistics
visualization
ORFs
genome
16 days ago by
marongiu.luigi
▴ 710
0
votes
0
replies
144
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
3 days ago by
4fzcgueyp5
• 0
0
votes
0
replies
119
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 4 days ago by
Ram
43k • written 4 days ago by
newuser2024
• 0
0
votes
0
replies
156
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
3 days ago by
avocado123
• 0
0
votes
0
replies
141
views
RNA-seq: full length gene
RNA-seq
updated 2 days ago by
Ram
43k • written 2 days ago by
Nargis
• 0
0
votes
0
replies
256
views
batch correction: cds from seurat
batch-correction
R
seurat
monocle3
cds
updated 19 days ago by
Ram
43k • written 20 days ago by
sooni
▴ 20
0
votes
1
reply
156
views
RNA-seq bacteria contamination
RNA-seq
updated 6 days ago by
GenoMax
141k • written 6 days ago by
sh
• 0
0
votes
0
replies
180
views
Pruning with plink finds a majority of SNPs in very high LD
LD
SNP
plink
pruning
10 days ago by
enferdeflame
• 0
0
votes
0
replies
1.8k
views
Differential expression using Scran batch corrected data
single-cell
Batch-effect
RNA-Seq
Scran
updated 10 days ago by
Ram
43k • written 5.5 years ago by
baldissera152
▴ 10
0
votes
0
replies
144
views
GWAS Phenotypes
GWAS
12 days ago by
solomoncharles77
▴ 90
0
votes
0
replies
357
views
Looking for an explanation as to what the Peak Score is from HOMER, not finding any answers on Biostars yet
Homer
ATAC-seq
11 days ago by
Ronin
• 0
0
votes
0
replies
75
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
6 days ago by
sativus
▴ 20
0
votes
0
replies
1.7k
views
Batch effect and CCA
CCA
RNA-Seq
seurat
batch-effect
updated 11 days ago by
Ram
43k • written 5.1 years ago by
akivab2
▴ 110
0
votes
4
replies
325
views
Questions about transfering wgs file to reference genome file
fasta
cram
genome
17 days ago by
me
• 0
0
votes
1
reply
1.2k
views
Controlling for batch effect in SNP-based PCA
whole-genome
PCA
batch-effect
SNP
updated 11 days ago by
Ram
43k • written 4.7 years ago by
Ace
▴ 90
0
votes
0
replies
116
views
Extracting Enhancer Regions from ENCODE Annotation Files
ENCODE
enhancer
25 days ago by
YamengWu
• 0
0
votes
1
reply
234
views
Need help with improving the 16S rRNA sequence quality with trimmomatic?
bioinformatic
Trimmomatic
updated 26 days ago by
gv
• 0 • written 29 days ago by
Kai Xin
• 0
0
votes
2
replies
2.8k
views
RNA-seq unbalanced batch effect correction
limma
RNA-Seq
edgeR
batch-effect
updated 10 days ago by
Ram
43k • written 7.0 years ago by
endikavarela
• 0
0
votes
0
replies
252
views
What does it means, when 2-direction perturbed pathways are identified in the gage enrichment analysis?
r
pathway
go-enrichment
gage
26 days ago by
Assa Yeroslaviz
★ 1.8k
0
votes
1
reply
251
views
Bowtie2 alignment rate
galaxy
Bowtie
alignment-rate
updated 26 days ago by
gv
• 0 • written 4 weeks ago by
pavithraashokkumar818
• 0
0
votes
0
replies
1.7k
views
Differential Gene Expression Analysis using two distinct scRNA-seq datasets
differential-gene-expression
RNA-Seq
scRNA-seq
updated 19 days ago by
Ram
43k • written 6.5 years ago by
Eskimo
▴ 120
0
votes
1
reply
300
views
Monotonic genes in results of differential gene expression analysis
differential-expression
RNA-seq
monotonic-genes
updated 19 days ago by
Ram
43k • written 3 months ago by
Shaimaa Gamal
▴ 10
0
votes
10
replies
640
views
Nextflow ERROR : Timeout waiting for connection from pool
nextflow
27 days ago by
dzisis1986
▴ 70
0
votes
1
reply
168
views
P-values for pairwise FST
FST
P-value
pairwise
updated 19 days ago by
dthorbur
★ 1.9k • written 19 days ago by
Emy
▴ 50
0
votes
1
reply
245
views
eQTL analysis of GWAS summary statistics, missing GT values
Genomics
eQTL
GWAS
updated 23 days ago by
Ram
43k • written 12 weeks ago by
Orlando
• 0
0
votes
1
reply
167
views
How do I run fastq-dump on multiple prefetched files at once?
sratoolkit
fastq-dump
updated 21 days ago by
Pierre Lindenbaum
161k • written 21 days ago by
biotrekker
▴ 100
0
votes
0
replies
1.5k
views
RIPSeeker viewRIP function fails to extract values() in GRangesList/S4 object
RIPSeq
S4
RIP
R
updated 11 days ago by
Ram
43k • written 6.2 years ago by
CrisMar
▴ 80
0
votes
1
reply
821
views
Bulk RNAseq MACS Sort Quality Contamination
EdgeR
Batch-effect
RNA-Seq
updated 10 days ago by
Ram
43k • written 3.7 years ago by
jordan15
• 0
0
votes
0
replies
147
views
how to read graph_test output of monocle 3
monocle3
3 days ago by
synat.keam
▴ 100
0
votes
1
reply
201
views
Annotating a dataset with gnomAD v4 using Hail
Python
Sequencing
Hail
Exome
Annotation
updated 11 days ago by
DKA
▴ 40 • written 11 days ago by
james.melhorn
• 0
0
votes
0
replies
146
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 2 days ago by
Ram
43k • written 2 days ago by
SineWave
• 0
0
votes
0
replies
1.1k
views
Should batch correction be performed before or after feature selection in scRNA-seq
batch-effect
scRNA-seq
feature-selection
updated 11 days ago by
Ram
43k • written 4.9 years ago by
Lucy
▴ 140
484 results • Page
4 of 10
Recent Votes
Comment: NGS forensics: how to know if data is fabricated
A: Hard time trying to calculate Allele Frequency and DP from Platypus
Answer: 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
Answer: NGS forensics: how to know if data is fabricated
Comment: NGS forensics: how to know if data is fabricated
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Answer: Finding batch and outlayers
by
Tigran
• 0
![enter image description here][1] [1]: /media/images/aa60b9ef-b08c-4093-9f0d-fb656a5c
Comment: NGS forensics: how to know if data is fabricated
by
benformatics
3.9k
Can you post an IGV screenshot of what this looks like?
Comment: NGS forensics: how to know if data is fabricated
by
benformatics
3.9k
Yeah some of the Illumina machines pre-trim adapters (not sure if this is still the standard). I've also definitely also seen quality-trimm…
Comment: PDB related issue
by
noodle
▴ 530
You can typically find much more useful info in the cif file, for example what you've found is called '_atom_site.pdbx_PDB_ins_code ' and d…
Comment: PDB related issue
by
Mensur Dlakic
★ 27k
The best way to find out is to read the original paper. My guess is that the residue has been crystallized in alternative conformations, wh…
Answer: NGS forensics: how to know if data is fabricated
by
Mensur Dlakic
★ 27k
I share the opinion by @philippbayer I have seen enough questionable things in life and in science to keep me permanently jaded, but there…
Comment: How many reads for WGS Sequencing?
by
Mensur Dlakic
★ 27k
I downloaded the data in two files from the link you provided. With this command: megahit -1 ERR072246_1.fastq.gz -2 ERR072246_2.fastq…
Comment: How many reads for WGS Sequencing?
by
Mensur Dlakic
★ 27k
If you have Linux the assembly should work on your system, but 8 GB is generally not enough for assembling larger genomes.
Comment: How many reads for WGS Sequencing?
by
Mensur Dlakic
★ 27k
I think you might be getting stuck on less relevant parts of my exercise. The most important point was that nothing is wrong with the data.…
Comment: What does it mean single base resolution in sequencing?
by
dsull
★ 5.9k
Great comprehensive explanation and overview of the technologies -- with regards to sequencing assays, the one thing I'd add is SNV identif…
Answer: What does it mean single base resolution in sequencing?
by
dsull
★ 5.9k
I think that term means slightly different things in different contexts. For example, it's useful to profile mRNA modifications (e.g. m6a) …
Comment: Cannot process all the reads in a fast5 file?
by
chujie
• 0
Hi, I met the same problem, have you found the solution?
Answer: What does it mean single base resolution in sequencing?
by
LauferVA
4.2k
Hi @fe3e6f65 , In a single sentence, the answer to your question can be summarized as, "*the resolution of a genomic technology refers to …
Comment: PCA plot
by
LauferVA
4.2k
Without more context, we cannot interpret this PCA plot. There are many possibilities. In addition, this question is basic enough that it w…
Comment: NGS forensics: how to know if data is fabricated
by
Jeremy Leipzig
22k
i have the name ready: out**liar**
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