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1,000 results • Page
4 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
206
views
miRDeep2: How to get the read counts
mirdeep2
14 days ago by
Atul K.
• 0
0
votes
0
replies
212
views
Lncipedia GTF file error
Proteomics
updated 13 days ago by
Ram
43k • written 14 days ago by
atharvakarkare14
▴ 30
3
votes
3
replies
511
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 13 days ago by
swbarnes2
14k • written 14 days ago by
noodle
▴ 580
0
votes
2
replies
571
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
14 days ago by
航太郎
• 0
0
votes
0
replies
225
views
create genewise sync file in popoolation
popoolation
updated 14 days ago by
GenoMax
142k • written 14 days ago by
N.Y.Wiyana-Hewage
• 0
0
votes
2
replies
403
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
14 days ago by
Ashok
• 0
0
votes
2
replies
443
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
14 days ago by
Ashok
• 0
0
votes
0
replies
225
views
Variant Generation Using Longshot
long-reads
variant-calling
ONT
minion
longshot
updated 14 days ago by
Ram
43k • written 14 days ago by
samuelkalandarov2002
▴ 10
0
votes
2
replies
451
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
13 days ago by
_quantum_girl_
▴ 10
0
votes
0
replies
216
views
traying to make a maf from an already annotated vcf
vcf
vcf2maf
maf
maftools
VEP
10 days ago by
Javier
• 0
0
votes
0
replies
195
views
Pruning with plink finds a majority of SNPs in very high LD
LD
SNP
plink
pruning
14 days ago by
enferdeflame
• 0
1
vote
1
reply
438
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
updated 12 days ago by
Gordon Smyth
★ 7.1k • written 14 days ago by
Chris
▴ 260
0
votes
1
reply
411
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree
microbiome
updated 14 days ago by
Ram
43k • written 19 months ago by
Muhammad
• 0
0
votes
0
replies
169
views
How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau-score
tspex
updated 14 days ago by
Ram
43k • written 15 days ago by
bioinfo223
▴ 10
0
votes
0
replies
188
views
How to root an unrooted tree with a known root tree?
phylogenetics
rooting
R
15 days ago by
P.
• 0
0
votes
0
replies
178
views
Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
snpEff
15 days ago by
ekirsch
• 0
1
vote
1
reply
471
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
13 days ago by
renan.igor
• 0
0
votes
0
replies
196
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
15 days ago by
synat.keam
▴ 100
0
votes
1
reply
290
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 15 days ago by
GenoMax
142k • written 15 days ago by
ycts
• 0
0
votes
4
replies
619
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
14 days ago by
Kai Xin
• 0
1
vote
1
reply
243
views
Retrieve a % coverage for each transcript
RNA-seq
updated 15 days ago by
Ram
43k • written 15 days ago by
jammydodger123456
▴ 40
0
votes
2
replies
401
views
How can I solve this error?
metal
15 days ago by
22211020193
• 0
0
votes
0
replies
179
views
Struggling to lift genome builds
PLINK
liftover
GWAS
updated 15 days ago by
GenoMax
142k • written 15 days ago by
srimmer
• 0
1
vote
2
replies
300
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 15 days ago by
Ram
43k • written 15 days ago by
aniigodwinn
• 0
0
votes
0
replies
364
views
Looking for an explanation as to what the Peak Score is from HOMER, not finding any answers on Biostars yet
Homer
ATAC-seq
15 days ago by
Ronin
• 0
2
votes
7
replies
891
views
Removing duplicates
duplicates
ONT
minimap2
updated 14 days ago by
noodle
▴ 580 • written 15 days ago by
quentinperriere
• 0
0
votes
1
reply
216
views
Annotating a dataset with gnomAD v4 using Hail
Python
Sequencing
Hail
Exome
Annotation
updated 15 days ago by
DKA
▴ 40 • written 15 days ago by
james.melhorn
• 0
0
votes
1
reply
204
views
Freyja plot error
Freyja
updated 15 days ago by
Ram
43k • written 16 days ago by
Adyasha
• 0
0
votes
0
replies
168
views
BIOM format can contain tabular data ?
BIOM
phyloseq
biomformat
R
16 days ago by
chemokine-1
▴ 10
0
votes
4
replies
544
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
15 days ago by
feather-W
• 0
0
votes
2
replies
266
views
Bedmethyl file format
bedmethyl
methylation
updated 15 days ago by
GenoMax
142k • written 16 days ago by
njornet
▴ 20
0
votes
0
replies
186
views
sequence table for DADA2 chimera filtering
OTU
sequencetable
DADA2
16 days ago by
Ali
• 0
2
votes
4
replies
347
views
SnpEff annotates coding duplication as intronic?
snpeff
16 days ago by
kirill.zaslavsky
• 0
0
votes
2
replies
279
views
Calculating percentage of cells proliferating in single cell rna seq data
statistics
scRNA-seq
proliferation
15 days ago by
mropri
▴ 150
0
votes
0
replies
158
views
Input into WGCNA and Error on constructNetworks on RNA-Seq data - unique rownames
rownames
RNA-Seq
WGCNA
unique
16 days ago by
shasabhi1
• 0
0
votes
0
replies
147
views
How to summarize dbCAN3 results
dbCAN
CAZy
CAZyme
dbCAN3
dbCAN2
16 days ago by
Nishat
• 0
0
votes
0
replies
175
views
what exactly is a k-mer table (remora)?
remora
basecall
16 days ago by
anne
• 0
1
vote
1
reply
196
views
Help/Direction Needed for Data Analysis of RNA
Sequencing
RNA-seq
DNA-Seq
updated 16 days ago by
dsull
★ 5.9k • written 16 days ago by
niruf
• 0
0
votes
0
replies
153
views
GWAS Phenotypes
GWAS
16 days ago by
solomoncharles77
▴ 90
0
votes
2
replies
343
views
GSEA analysis in R
GSEA
R
Arabidopsis
15 days ago by
Sudip
• 0
0
votes
0
replies
129
views
Add geno header to VariantAnnotation objects
nichenet
scRNA-seq
17 days ago by
QX
• 0
2
votes
5
replies
520
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats
hg002
bed
homopolymer-regions
16 days ago by
Bikram Kumar
• 0
0
votes
2
replies
281
views
Statistical Advice Needed for RNAseq Data Analysis
Statistical-Significance
Genomics
RNA-seq
Data-Analysis
updated 16 days ago by
Ram
43k • written 17 days ago by
David
• 0
1
vote
2
replies
293
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq
kallisto
16 days ago by
bioinfo
▴ 150
0
votes
1
reply
208
views
How to get the reference panel sites for TOPMed hg37 and 38
Imputation
updated 17 days ago by
bk11
★ 2.4k • written 17 days ago by
sinhas
• 0
0
votes
1
reply
228
views
merging Seurat objects after SCT
Seurat
SCT
updated 17 days ago by
Ram
43k • written 17 days ago by
michelle.swarovski
• 0
0
votes
1
reply
240
views
Two databases: Human Microbiome Project and MGnify
Microbiome
databases
updated 17 days ago by
GenoMax
142k • written 17 days ago by
haiying.kong
▴ 360
0
votes
2
replies
292
views
RNAseq 1 control 2 different treatment
RNA-seq
17 days ago by
matteo.levorato
• 0
1
vote
0
replies
152
views
Seeking Advice on Gene Ontology Analysis for Bulk RNA-Seq Data Without Control Samples
Gene-ontology
RNA-seq
R
updated 17 days ago by
Ram
43k • written 17 days ago by
Oscar
▴ 10
2
votes
0
replies
218
views
What are good Python models/packages to predict small molecula (SMILES) binding to proteins ?
SMILES
17 days ago by
Alexander
▴ 220
1,000 results • Page
4 of 20
Recent Votes
Answer: How many reads for WGS Sequencing?
Answer: How many reads for WGS Sequencing?
Comment: How to Calulate Allele Frequency from a VCF File?
Answer: Introduce SNPs on FASTA
Answer: how to split multi-fasta file into single fasta file named by header
How to Calulate Allele Frequency from a VCF File?
Answer: allele frequency in VCF
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Recent Replies
Comment: What analysis suitable to identify similarly expressed genes between two samples
by
ATpoint
82k
Can you post your setup, so how many groups and their replication number? I can tell you by experience that you need even more replication …
Answer: DSEQ2 analysis
by
ATpoint
82k
The tool is called D**E**Seq2. Anyway, if your factor is `factor(conditions, levels = c("control", "mutant"))` then the first level is the …
Comment: Odd alignment question/finding
by
barslmn
★ 2.1k
Maybe it is caused by fastp. https://github.com/OpenGene/fastp/issues/506
Comment: Generating mpileup file using samtools
by
Joe
21k
It's been a long time since I did this sort of thing, but I have a vague recollection that the mpileup process was made simpler and/or roll…
Comment: Introduce SNPs on FASTA
by
Riccardo
▴ 10
Thank you very much for your answer!
Comment: how to split multi-fasta file into single fasta file named by header
by
rsieber
▴ 10
This is great also for multiline fastas
Comment: how to split multi-fasta file into single fasta file named by header
by
rsieber
▴ 10
This only works for the first line of sequences.
Answer: What purposes can TPM values be used for?
by
b.contreras.moreira
▴ 180
In case it helps: https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units
Comment: What analysis suitable to identify similarly expressed genes between two samples
by
alifafiq1
• 0
Thank you @AT point. I was planning to use DESeq2 and use the alternate hypothesis (lessAbs) too considering that is the only package that …
Comment: Does comparing two different groups to a common third group introduce bias in th
by
ATpoint
82k
Note that by basic algebra A vs C and B vs C is the same as A vs B, so you might rethink your analysis to answer your question in a much si…
Comment: RNAseq one control two conditions, shared and exclusive genes
by
Mohamed Abderrahmane
▴ 20
Yes, why not? If it works for you like that, bingo!
Answer: Does comparing two different groups to a common third group introduce bias in th
by
christopher medway
▴ 450
You are testing groups A and B to a common baseline (C) - I don't see that there is anything wrong with doing that. It is a fairly common a…
Comment: HOMER on AWS
by
clairechung112
• 0
Hi. I guess it is solved by now, but as I did not find the answer immediately online, here is the answer I posted on a relevant question: h…
Answer: homer not configured properly
by
clairechung112
• 0
A late reply, but I just solved exactly the same error upon a request in the team. Please see if it helps in case anyone meets the same err…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
Chris Dean
▴ 390
Was the spike-in a commercial product, e.g., from Zymo? Can you provide more information about what cells or DNA was spiked into your samp…
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