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
Profile
Posts
Awards
Show
all
questions
tools
blogs
news
tutorials
forum
answers
comments
1
vote
0
replies
1.0k
views
Comment:
Comment: How to add a individuals IDs to admixture output?
5 months ago by
rimgubaev
▴ 280
1
vote
1
reply
594
views
Which SNP callers are suitable for QTL mapping in GBS experiments with low coverage?
SNP
QTL-mapping
GBS
SNP caller
low-coverage
5 months ago by
rimgubaev
▴ 280
1
vote
0
replies
594
views
Answer:
Answer: Which SNP callers are suitable for QTL mapping in GBS experiments with low cover
5 months ago by
rimgubaev
▴ 280
0
votes
0
replies
765
views
Answer:
Answer: QTL mapping by GBS
5 months ago by
rimgubaev
▴ 280
0
votes
0
replies
3.3k
views
Answer:
Answer: GBS SNPs calling
5 months ago by
rimgubaev
▴ 280
0
votes
0
replies
671
views
Answer:
Answer: Best (GATK compatible) RadSeq/GBS pipeline in 2021
5 months ago by
rimgubaev
▴ 280
2
votes
3
replies
1.0k
views
How to add a individuals IDs to admixture output?
admixture
population genetics
5 months ago by
rimgubaev
▴ 280
3
votes
5
replies
3.3k
views
Could somebody suggest free pathway visualization tool for omics data from plants?
Vizualization
Pathways
RNA-Seq
updated 16 months ago by
bigmawen
▴ 430 • written 4.1 years ago by
rimgubaev
▴ 280
0
votes
0
replies
321
views
How to formally test the replicate consistency having genotype data?
SNP
genetic variance
replicates
vcf
consistency
17 months ago by
rimgubaev
▴ 280
0
votes
0
replies
668
views
Are there tools for SNP remapping (liftover) for non-model organism or ones that do not require chain file?
SNP
liftover
assembly
chain file
vcf
21 months ago by
rimgubaev
▴ 280
0
votes
2
replies
701
views
What tools to use for genetic map construction or marker ordering using large SNP datasets?
GBS
SNP
Genetic map
Marker ordering
QTL
2.2 years ago by
rimgubaev
▴ 280
0
votes
0
replies
466
views
Comment:
C: How to calculate number of positions covered by at least 10 times in bam file?
2.3 years ago by
rimgubaev
▴ 280
0
votes
0
replies
466
views
Comment:
C: How to calculate number of positions covered by at least 10 times in bam file?
2.3 years ago by
rimgubaev
▴ 280
4
votes
4
replies
466
views
How to calculate number of positions covered by at least 10 times in bam file?
coverage
bam
alignment
bedtools
awk
updated 2.3 years ago by
ATpoint
64k • written 2.3 years ago by
rimgubaev
▴ 280
1
vote
0
replies
567
views
How to liftover SNPs between different assemblies from different databases?
SNP
liftover
ENSEMBL
NCBI
Assembly
updated 2.4 years ago by
Biostar
20 • written 2.5 years ago by
rimgubaev
▴ 280
0
votes
0
replies
16k
views
Comment:
C: intersect VCF files
2.5 years ago by
rimgubaev
▴ 280
0
votes
2
replies
877
views
How to obtain an annotation for the list of NCBI's Gene ID?
NCBI
GeneID
annotation
2.6 years ago by
rimgubaev
▴ 280
0
votes
0
replies
534
views
Which option is better for variance component estimation in TASSEL?
TASSEL
GWAS
Variance
P3D
MLM
updated 2.6 years ago by
Biostar
20 • written 2.6 years ago by
rimgubaev
▴ 280
3
votes
5
replies
1.9k
views
Tools to filter the heterozygous SNPs with biased allele depth (AD) values in vcf file.
vcf
GATK
heterozygous SNPs
Allele depth
AD
updated 16 months ago by
Pierre Lindenbaum
147k • written 2.6 years ago by
rimgubaev
▴ 280
0
votes
0
replies
624
views
Heterozygous calls (SNPs) problem while working with inbred lines.
SNPs
heterozygous
GATK
Sequencing errors
vcf
2.6 years ago by
rimgubaev
▴ 280
0
votes
0
replies
3.8k
views
Comment:
C: Using Gatk On Inbred Species - What To Do With The Heterozygous Calls?
2.6 years ago by
rimgubaev
▴ 280
0
votes
1
reply
411
views
Comment:
C: Is it ok to use median instead of mean for phenotype data in GWAS studies?
2.6 years ago by
rimgubaev
▴ 280
0
votes
3
replies
411
views
Is it ok to use median instead of mean for phenotype data in GWAS studies?
GWAS
association
phenotype data
2.6 years ago by
rimgubaev
▴ 280
0
votes
0
replies
487
views
What is optimal distance to scan for genes near SNPs for pathway overrepresentation analysis?
pathway analysis
pathways
GWAS
SnpEff
SNP
2.7 years ago by
rimgubaev
▴ 280
0
votes
0
replies
694
views
How to annotate only closest SNP using SnpEff?
SnpEff
annotation
SNP
2.7 years ago by
rimgubaev
▴ 280
0
votes
0
replies
803
views
Tools and pipelines for bulk segregant analysis (BSA) in combination with genotyping-by-sequencing (GBS) techniques.
Association mapping
BSA
GBS
2.7 years ago by
rimgubaev
▴ 280
0
votes
0
replies
370
views
How many Individuals should I use in order to define haploblocks?
Haploblocks
Population genetics
Sample size
LD
2.7 years ago by
rimgubaev
▴ 280
0
votes
1
reply
545
views
Comment:
C: How to select SNPs for haploblock identification after GWAS analysis?
2.7 years ago by
rimgubaev
▴ 280
5
votes
3
replies
545
views
How to select SNPs for haploblock identification after GWAS analysis?
GWAS
Haploblocks
SNP
updated 2.7 years ago by
Kevin Blighe
82k • written 2.7 years ago by
rimgubaev
▴ 280
0
votes
1
reply
4.4k
views
Comment:
C: How to make Q-Q plots for different models at a single chart using R?
2.7 years ago by
rimgubaev
▴ 280
7
votes
6
replies
4.4k
views
How to make Q-Q plots for different models at a single chart using R?
GWAS
qqman
Q–Q plot
model selection
updated 9 months ago by
waqaskhokhar999
▴ 130 • written 2.7 years ago by
rimgubaev
▴ 280
3
votes
0
replies
3.1k
views
Answer:
A: How to add a custom chromosome labels in qqman R package?
2.7 years ago by
rimgubaev
▴ 280
5
votes
2
replies
3.1k
views
How to add a custom chromosome labels in qqman R package?
qqman
GWAS
manhattan plot
chromosome labels
2.7 years ago by
rimgubaev
▴ 280
0
votes
0
replies
2.9k
views
Comment:
C: What suggestive line at manhattan plot usually stands for?
2.7 years ago by
rimgubaev
▴ 280
1
vote
2
replies
2.9k
views
What suggestive line at manhattan plot usually stands for?
GWAS
Manhattan plot
Multiple testing correction
2.7 years ago by
rimgubaev
▴ 280
0
votes
0
replies
2.3k
views
Comment:
C: Haplotypes For Each Sample
2.7 years ago by
rimgubaev
▴ 280
1
vote
1
reply
589
views
Could someone recommend courses/workshops on plant quantitative genetics?
Plant Genomics
GWAS
QTL mapping
courses
workshops
2.8 years ago by
rimgubaev
▴ 280
0
votes
2
replies
533
views
Is there any command line or GUI software to find SSR microsatellites using pattern?
SSR
microsatellites
Hordeum vulgare
updated 2.8 years ago by
Pierre Lindenbaum
147k • written 2.8 years ago by
rimgubaev
▴ 280
0
votes
0
replies
1.3k
views
Comment:
C: How to extract promoter sequences from a plant draft genome?
2.9 years ago by
rimgubaev
▴ 280
2
votes
2
replies
1.3k
views
Comment:
C: How to extract promoter sequences from a plant draft genome?
2.9 years ago by
rimgubaev
▴ 280
0
votes
1
reply
1.2k
views
Why kinship is a random effect while population structure is a fixed effect in GWAS studies?
Kinship matrix
Principle components
GWAS
MLM
2.9 years ago by
rimgubaev
▴ 280
0
votes
0
replies
1.3k
views
What kind of approaches are used in order to estimate average size of LD block using LD-decay plot?
SNP
Linkage disequilibrium
R2
LD block
2.9 years ago by
rimgubaev
▴ 280
3
votes
1
reply
16k
views
Comment:
C: intersect VCF files
2.9 years ago by
rimgubaev
▴ 280
0
votes
0
replies
735
views
How to convert vcf to SPAGeDi input format?
SPAGeDi
VCF
Kinship
updated 2.9 years ago by
Biostar
20 • written 3.1 years ago by
rimgubaev
▴ 280
0
votes
0
replies
507
views
What does the exclamation mark (!) means in Haploview output?
Haploview
haploblocks
LD
3.0 years ago by
rimgubaev
▴ 280
0
votes
0
replies
533
views
Is it possible to assign haplotypes to individuals using haploview?
Haploview
haplotype blocks
LD
vcf
plink
3.0 years ago by
rimgubaev
▴ 280
0
votes
0
replies
1.9k
views
How to interpret Centred IBS kinship matrix produced by TASSEL?
Kinship
Centered IBS
TASSEL
3.1 years ago by
rimgubaev
▴ 280
0
votes
0
replies
601
views
Comment:
C: Is it ok to use genotype replicates for association studies?
3.1 years ago by
rimgubaev
▴ 280
1
vote
3
replies
601
views
Is it ok to use genotype replicates for association studies?
GWAS
permutation test
TASSEL
3.1 years ago by
rimgubaev
▴ 280
0
votes
1
reply
830
views
Comment:
C: How to make association studies using haplotype (LD) blocks instead of SNPs?
3.1 years ago by
rimgubaev
▴ 280
101 results • Page
1 of 3
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