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1,000 results • Page
3 of 20
Sort: Views
Rank
Views
Votes
Replies
2
votes
8
replies
2.9k
views
How to convert a database from protein to nucleotide
blastn
unix
blastx
blast
updated 11 months ago by
Ram
43k • written 7.1 years ago by
AJTrunkskun94
• 0
0
votes
7
replies
2.9k
views
qPCR: Huge variation in fold change of genes between biological replicates
qpcr
fold-change
updated 7 months ago by
Ram
43k • written 5.9 years ago by
AP
▴ 80
1
vote
3
replies
2.9k
views
Multiple Sequence Alignment Python
multiple-sequence-alignment
ClustalW
Biopython
updated 11 months ago by
Ram
43k • written 6.0 years ago by
Manu Madhavan
▴ 20
0
votes
0
replies
2.8k
views
TCGA RNAseqVer2 batch effects
TCGA
RNA-Seq
batch-effect
updated 11 days ago by
Ram
43k • written 8.6 years ago by
annadv
• 0
1
vote
1
reply
2.8k
views
Comparing time series expression data
time-series
gene-expression
updated 11 months ago by
Ram
43k • written 6.7 years ago by
The
▴ 180
0
votes
2
replies
2.8k
views
RNA-seq unbalanced batch effect correction
limma
RNA-Seq
edgeR
batch-effect
updated 9 days ago by
Ram
43k • written 7.0 years ago by
endikavarela
• 0
0
votes
3
replies
2.8k
views
Circos plot for ecoli genome
rna-seq
circos
updated 8 months ago by
Ram
43k • written 7.4 years ago by
raya.girish
▴ 30
1
vote
4
replies
2.8k
views
removing confounding batch effect with RUVseq
RUVseq
RNA-Seq
batch-effect
DESeq2
updated 10 days ago by
Ram
43k • written 5.1 years ago by
grant.hovhannisyan
★ 2.6k
0
votes
3
replies
2.8k
views
Generate GTF/GFF file (coordinates) from a FASTA annotated file.
Assembly
genome
updated 11 months ago by
Ram
43k • written 4.6 years ago by
marquezg48
• 0
0
votes
4
replies
2.8k
views
Music Tool Integration To Galaxy Ngs
music
galaxy
updated 10 months ago by
Ram
43k • written 10.1 years ago by
Chetan Joshi
▴ 20
0
votes
1
reply
2.8k
views
Can't make sva comparison despite very distinct batch effects
sva
batch-effect
updated 10 days ago by
Ram
43k • written 6.2 years ago by
jjrin
▴ 40
1
vote
1
reply
2.8k
views
Hmmer Alignment input parse error
alignment
hmmer
updated 11 months ago by
Ram
43k • written 6.8 years ago by
hivemind
▴ 20
3
votes
3
replies
2.8k
views
WGCNA Labeled Heatmap
heatmap
wgcna
updated 7 months ago by
Ram
43k • written 2.6 years ago by
Anand
▴ 40
0
votes
5
replies
2.8k
views
Visualize VarScan2 Copy Number Aberrations in IGV
VarScan2
sequence
alignment
IGV
updated 10 months ago by
Ram
43k • written 8.0 years ago by
plumgwodehouse
• 0
2
votes
3
replies
2.7k
views
Merge really large amount of Seurat objects
Seurat
10 months ago by
Andy
▴ 120
0
votes
0
replies
2.7k
views
Are secondary alignments (SAM) produced by STAR aligner linked with MAPQ score?
alignment
RNA-Seq
updated 11 months ago by
Ram
43k • written 7.1 years ago by
Claudio
• 0
0
votes
2
replies
2.7k
views
How to get Haplotype file from PLINK format data
SNP
PLINK
updated 11 months ago by
Ram
43k • written 6.0 years ago by
bha
▴ 80
0
votes
1
reply
2.7k
views
how to read h5 file in Seurat if its structure is not like 10x h5 file structure?
RNA-Seq
single-cell
scRNA-seq
Seurat
R
updated 8 months ago by
Ram
43k • written 2.4 years ago by
fifty_fifty
▴ 60
0
votes
4
replies
2.7k
views
MACS2 BAMPE and BEDPE gave dramatically different "mean fragment size"
ChIP-Seq
updated 4 weeks ago by
axol0tl
• 0 • written 6.5 years ago by
Xinwei Han
• 0
1
vote
3
replies
2.7k
views
g++: error:unrecognized command line option ‘-std=c++2a’
gcc
updated 11 months ago by
Rob
6.5k • written 11 months ago by
wangjincheng
• 0
1
vote
1
reply
2.7k
views
Plotting a PCA Plot from SVASeq results
pca
ruvseq
sva
svaseq
batch-effect
updated 11 days ago by
Ram
43k • written 6.2 years ago by
jjrin
▴ 40
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression
RNA-Seq
GTex
DESeq2
updated 18 days ago by
Ram
43k • written 6.4 years ago by
vikram
▴ 10
0
votes
0
replies
2.7k
views
GROMACS RMSD COMMANDS
gromacs
updated 10 months ago by
Ram
43k • written 8.3 years ago by
adammbbs
▴ 10
0
votes
0
replies
2.7k
views
Comparing lists generated by Counter() and .most_common() for AA seqs
python
amino-acid
updated 11 days ago by
Ram
43k • written 9.9 years ago by
st.ph.n
★ 2.7k
1
vote
5
replies
2.7k
views
Calculating distance matrix of RNA-seq data
Dynamic-Time-Warping
R
time-series
updated 11 months ago by
Ram
43k • written 6.1 years ago by
zizigolu
★ 4.3k
1
vote
1
reply
2.7k
views
trinity assembly error, run failed
trinity
rna-seq
updated 8 months ago by
Ram
43k • written 7.9 years ago by
nikelle.petrillo
▴ 110
4
votes
7
replies
2.7k
views
low bootstrap value?
phylogeny
genome
alignment
updated 11 months ago by
Ram
43k • written 4.9 years ago by
Kumar
▴ 120
4
votes
14
replies
2.7k
views
Is it possible to annotate single genes by snpeff
snp
vcf
updated 10 months ago by
Ram
43k • written 6.7 years ago by
misbahabas
▴ 70
0
votes
1
reply
2.6k
views
get counts by gene for single cell rna seq
scRNA-seq
single-cell
updated 10 months ago by
Ram
43k • written 3.2 years ago by
das2000sidd
▴ 30
2
votes
4
replies
2.6k
views
DESeq2 inconsistent results
differential-gene-expression
RNA-Seq
DESeq2
updated 18 days ago by
Ram
43k • written 8.1 years ago by
Chris Gene
▴ 80
4
votes
9
replies
2.6k
views
Blast+ remote database names
blast
remote
databases
Blastplus
updated 9 months ago by
GenoMax
141k • written 2.3 years ago by
Komalharini
• 0
0
votes
0
replies
2.6k
views
monocle clustering cells without marker genes error
R
RNA-Seq
monocle
updated 10 months ago by
Ram
43k • written 5.7 years ago by
hsu
▴ 40
0
votes
7
replies
2.6k
views
How to perform gene annotation in kallisto?
Gene
kallisto
annotation
updated 8 months ago by
호성
• 0 • written 2.7 years ago by
synat.keam
▴ 100
4
votes
6
replies
2.6k
views
Convert Nanopore Fast5 files to Fasta format
fast5
fasta
Nanopore
11 months ago by
Sowmya Pulapet
▴ 70
1
vote
0
replies
2.6k
views
Running Multiple Alignments in MEGA with a script produces errors.
next-gen
RNA-Seq
MEGA
multiple-alignment
updated 11 months ago by
Ram
43k • written 8.1 years ago by
rachelrodgers12
▴ 10
1
vote
4
replies
2.6k
views
Using a Multiple Seq Alignment tool for pairwise alignments possible?
multiple-sequence-alignment
msa
alignment
updated 11 months ago by
Ram
43k • written 8.0 years ago by
nchuang
▴ 260
0
votes
3
replies
2.6k
views
Picard's Tool MarkDuplicates problem
picard
updated 10 months ago by
Ram
43k • written 4.2 years ago by
harmadikemil
• 0
0
votes
0
replies
2.6k
views
Removing batch effects from methylation beta values for molecular subtyping/cluster analysis
clustering
beta-values
batch-effect
methylation
updated 11 days ago by
Ram
43k • written 6.7 years ago by
alecmchiu
• 0
3
votes
7
replies
2.6k
views
6 follow
Online BLAST search using R
BLAST
R
updated 10 weeks ago by
SequenceServer
▴ 140 • written 2.7 years ago by
accibio
▴ 20
0
votes
4
replies
2.5k
views
picard markduplicate output smaller file
picard
markduplicates
gatk
updated 11 months ago by
Ram
43k • written 5.3 years ago by
Peter Chung
▴ 200
0
votes
3
replies
2.5k
views
PLINK can't find my files?
software-error
plink
windows
SNP
updated 4 months ago by
irene.treccani.work
• 0 • written 7.5 years ago by
stephanie.langevin
• 0
0
votes
6
replies
2.5k
views
Variable read length distribution after cutadapt running for my ATAC-seq datasets
cutadapt
read-length
alignment
ATAC-seq
updated 10 months ago by
Ram
43k • written 4.0 years ago by
yaoyao20152031
• 0
1
vote
4
replies
2.5k
views
MesKit error message - Join columns must be present in data.
MesKit
R
updated 10 months ago by
bataibence
• 0 • written 15 months ago by
CH1374
▴ 10
0
votes
3
replies
2.5k
views
Create small BAM file with pysam and iterate over reads
samtools
bam
pysam
updated 10 months ago by
Ram
43k • written 6.5 years ago by
lebedana21
• 0
2
votes
1
reply
2.5k
views
Converting blastn output to VCF (for SNPs): what is the quickest way?
VCF
blast
SNP
xml
updated 9 months ago by
Ram
43k • written 6.0 years ago by
Matteo Schiavinato
★ 3.6k
1
vote
1
reply
2.5k
views
problem with updating trinity
software-error
trinity
updated 10 months ago by
Ram
43k • written 5.4 years ago by
ashokkumar.mb
• 0
1
vote
8
replies
2.5k
views
Using NCBIs EDirect to download pubmed abstract
edirect
pubmed
NCBI
updated 10 months ago by
Ram
43k • written 5.8 years ago by
zorn21g
• 0
0
votes
0
replies
2.5k
views
Analysis and tools for gene/pathway conservation
evolution
updated 10 months ago by
Ram
43k • written 9.1 years ago by
hbw
▴ 90
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink
PED
updated 5 days ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
1
vote
8
replies
2.5k
views
subset data problem
R
seurat
9 months ago by
Andy
▴ 120
1,000 results • Page
3 of 20
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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Answer: ChIP-seq datasets: input samples omitted?
by
ATpoint
82k
In my hands (and from what I know based on many years here) inputs are almost exclusively used during peak calling to correct for loci-spec…
Comment: How to assign cell types after integration in scRNA
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82k
No difference here. After all you typically want a label per cluster/group, so either subset to the control condition to do the assignment,…
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Answer: How many reads for WGS Sequencing?
by
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★ 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
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22k
the samples that are `./.` have no coverage (or not enough to call a genotype) and the `0/0` are homozygous reference
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by
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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…
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by
zihanss
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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
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★ 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…
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