Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : this month
all time
today
this week
this month
this year
489 results • Page
3 of 10
Sort: Views
Rank
Views
Votes
Replies
0
votes
0
replies
734
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
RNA-Seq
scRNA-Seq
batch-effect
updated 9 days ago by
Ram
43k • written 3.4 years ago by
hkarakurt
▴ 180
0
votes
0
replies
733
views
"No group or design set" with deAna() function in EnrichmentBrowser package
RNA-Seq
R
EnrichmentBrowser
updated 10 days ago by
Ram
43k • written 4.1 years ago by
yxswhx
• 0
8
votes
10
replies
712
views
bash script
whole-genome-sequencing
updated 12 days ago by
Ram
43k • written 19 days ago by
bestone
▴ 30
2
votes
5
replies
694
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 7 days ago by
Jesse
▴ 740 • written 8 days ago by
Ann
★ 2.4k
2
votes
5
replies
673
views
samtools mpileup taking too long
Bam
samtools
sam
alignment
updated 22 days ago by
Ram
43k • written 6 weeks ago by
K
• 0
1
vote
0
replies
673
views
Conditions for valid batch effect correction
r
batch-effect
updated 11 days ago by
Ram
43k • written 5.2 years ago by
Sebastian Hesse
▴ 340
1
vote
1
reply
660
views
Save experiment with batch effects - Protein microarray
statistics
protein-array
batch-effect
updated 11 days ago by
Ram
43k • written 4.4 years ago by
s.lima.diogenes
▴ 10
0
votes
1
reply
658
views
How to fix FreeBayes error "unable to find FASTA index entry for bed files"
freebayes
variant-calling
RNA-Seq
updated 25 days ago by
Ram
43k • written 13 months ago by
wlei091226
• 0
0
votes
1
reply
656
views
How to find the co ordinates of long reads (simulated by Badreads) with respect to the reference genome
long-reads
reference-genome
assembly
updated 22 days ago by
Ram
43k • written 2.7 years ago by
Ashi
▴ 20
0
votes
0
replies
650
views
METAL GWAS
allele-frequency
gwas
updated 25 days ago by
Ram
43k • written 2.4 years ago by
晗颖
• 0
0
votes
10
replies
639
views
Nextflow ERROR : Timeout waiting for connection from pool
nextflow
26 days ago by
dzisis1986
▴ 70
2
votes
6
replies
637
views
Overlapping and merging ChIP-seq peaks
MACS2
HOMER
ChIP-seq
peak-calling
updated 25 days ago by
Ram
43k • written 4 months ago by
zea
• 0
1
vote
2
replies
634
views
Nanopore multisample variant calling
SNPs
nanopore
SNP-calling
variants
multisample
29 days ago by
colindaven
6.4k
2
votes
2
replies
631
views
Batch correction for DE analysis
batch-correction
mRNA
RNA-seq
DEGs
MDSplot
updated 11 days ago by
Ram
43k • written 2.6 years ago by
Yoonji
▴ 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 25 days ago by
Ram
43k • written 12 months ago by
Beatriz
• 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
28 days ago by
Ronin
• 0
0
votes
3
replies
619
views
Not all variants are annotated with AF - expected or a problem?
Variant-Calling
WGS
Alignment
updated 25 days ago by
Ram
43k • written 7 months ago by
Luiz
▴ 30
0
votes
6
replies
616
views
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
differential-expression
RNA-Seq
ONT
Nanopore
updated 18 days ago by
Ram
43k • written 5 months ago by
tw_140
• 0
1
vote
1
reply
599
views
accessing the global gut microbial gene catalogue (MEDUSA)
medusa
gene-catalogue
gut-microbiome
updated 16 days ago by
Ram
43k • written 3.2 years ago by
ramin.k2013
• 0
0
votes
9
replies
593
views
99.9999% of Q30 bases is normal?
RNA-seq
fastp
updated 16 days ago by
LauferVA
4.2k • written 17 days ago by
Aki
▴ 10
0
votes
0
replies
593
views
Avoid genome circularization with Canu assembler
circularization
ONT
Canu
repetitive-regions
assembler
updated 22 days ago by
Ram
43k • written 2.9 years ago by
Maria
• 0
0
votes
4
replies
584
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
8 days ago by
Kai Xin
• 0
0
votes
2
replies
579
views
Bacterial contamination in human DNA sample
Long-read-sequencing
Bacterial-contamination
updated 22 days ago by
Ram
43k • written 22 months ago by
priya.bmg
▴ 60
4
votes
9
replies
575
views
variant calling
variant-calling
updated 24 days ago by
Ram
43k • written 25 days ago by
dalibenam64
• 0
4
votes
7
replies
571
views
Can any JBrowse2 tracks show multiple colors for reads at different nucleotide positions?
JBrowse
JBrowse2
updated 26 days ago by
cmdcolin
★ 3.8k • written 29 days ago by
I0110
▴ 140
4
votes
7
replies
557
views
DESeq2 Multifactor Design
RNA-seq
DESeq2
updated 14 days ago by
Ram
43k • written 15 days ago by
AHerik
▴ 20
0
votes
6
replies
555
views
PacBio adapters in transcriptome assembly from short read data?
adapter
transcriptome
sequencing
pacbio
vecscreen
12 days ago by
Dunois
★ 2.5k
0
votes
1
reply
553
views
Differential Expression Analysis for miRNA
limma
Differential-gene-Expression
miRNA
updated 18 days ago by
Ram
43k • written 2.9 years ago by
Al
• 0
1
vote
0
replies
543
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
7 days ago by
mathavanbioinfo
▴ 90
0
votes
5
replies
542
views
seg fault, core dumped with manta 1.6.0
manta
gdb
updated 19 days ago by
Ram
43k • written 23 days ago by
Greg
• 0
0
votes
2
replies
542
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
9 days ago by
航太郎
• 0
0
votes
2
replies
541
views
autodockvina
python
python3
autodock
updated 9 days ago by
Ram
43k • written 4 months ago by
iamsmor
• 0
1
vote
1
reply
540
views
GEO analysis with R
R
updated 25 days ago by
Ram
43k • written 2.3 years ago by
abdalla.m
• 0
3
votes
12
replies
534
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
25 days ago by
Lila M
★ 1.2k
0
votes
1
reply
516
views
Geneious vs Perl script of IN SILICO PCR
PCR
Geneious
updated 25 days ago by
Ram
43k • written 23 months ago by
Bio_Crap
• 0
0
votes
2
replies
513
views
Gene expression assay Yeast sample prep
Live-cells
updated 25 days ago by
Ram
43k • written 22 months ago by
dshdixit
▴ 10
0
votes
11
replies
508
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
2 days ago by
atowns21
• 0
0
votes
4
replies
508
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
9 days ago by
feather-W
• 0
0
votes
5
replies
492
views
How to assure that sequence consensus is genuine?
genome
21 days ago by
marongiu.luigi
▴ 710
1
vote
1
reply
478
views
Manta: What does all this mean
manta
Variant-calling
VEP
updated 25 days ago by
Ram
43k • written 9 months ago by
josh.mannheimer
• 0
0
votes
0
replies
475
views
How to map Uniref90 genes (IDs) to Antibiotic resistant genes databases?
CARD
metagenomics
Humann2
antibiotic-resistant-genes
uniref
updated 16 days ago by
Ram
43k • written 2.0 years ago by
ramin.k2013
• 0
3
votes
3
replies
474
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 7 days ago by
swbarnes2
14k • written 9 days ago by
noodle
▴ 520
1
vote
1
reply
466
views
PLINK multivariable GLM output: p-value without BETA and SE
linear-model
glm
plink
updated 19 days ago by
chrchang523
10k • written 19 days ago by
dsbusiness135
▴ 10
0
votes
6
replies
464
views
Error in running Mauve alignner in Ubuntu 20.04
java
linux
aligner
mauve
17 days ago by
marongiu.luigi
▴ 710
0
votes
3
replies
459
views
How do I get the gene annotations as a text file from a genbank file?
sequence-annotation
genbank
updated 29 days ago by
Ram
43k • written 29 days ago by
eae6d2e7
• 0
2
votes
5
replies
459
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats
hg002
bed
homopolymer-regions
10 days ago by
Bikram Kumar
• 0
2
votes
5
replies
457
views
Marking duplicates using UMIs
Deduplication
UMI
updated 5 days ago by
i.sudbery
19k • written 7 days ago by
Lipika
• 0
0
votes
1
reply
455
views
principal coordinate analysis
PCoA
R
updated 25 days ago by
Ram
43k • written 10 months ago by
rene.j.erhardt
▴ 20
0
votes
1
reply
449
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 2 days ago by
ginellegrenier
• 0 • written 4 months ago by
Clayton
• 0
0
votes
0
replies
447
views
Tools for identifying trans-splicing from long read data
long-read
splicing
nanopore
trans-splicing
updated 22 days ago by
Ram
43k • written 14 months ago by
dthorbur
★ 1.9k
489 results • Page
3 of 10
Recent Votes
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
correcting for a batch in DESeq2
Recent Locations •
All
USA,
1 minute ago
Australia,
4 minutes ago
China,
8 minutes ago
United States,
11 minutes ago
Palau,
11 minutes ago
Bangladesh,
14 minutes ago
United States,
16 minutes ago
Recent Awards •
All
Teacher
to
Wayne
★ 2.0k
Popular Question
to
a_bis
▴ 40
Popular Question
to
anna
▴ 20
Popular Question
to
rohitsatyam102
▴ 850
Popular Question
to
candron
▴ 10
Scholar
to
Alex Reynolds
35k
Popular Question
to
chaco001
▴ 40
Recent Replies
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…
Answer: absolute path for symbolic links in Snakefile
by
Jesse
▴ 740
It's nothing to do with Snakemake, just the ordinary confusion of making relative symlinks when your working directory is somewhere else. …
Answer: Hide positions in alignment with 99% "–" characters to ignore single sequence in
by
Jesse
▴ 740
[seqmagick](https://github.com/fhcrc/seqmagick/) has a `--squeeze-threshold` option that does just this. For example with an MSA of five s…
Traffic: 1540 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