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Answer: Answer: Sample size, GxE GWAS
2.3 years ago by rimgubaev ▴ 340
1
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0
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798
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Comment: Comment: Interpretation of results obtained in GWAS analysis using MLMM
2.4 years ago by rimgubaev ▴ 340
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2
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1.9k
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Answer: Answer: Why don't my map files contain cM values?
2.4 years ago by rimgubaev ▴ 340
1
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0
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2.3k
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Comment: Comment: How to add a individuals IDs to admixture output?
3.2 years ago by rimgubaev ▴ 340
1
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1
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1.2k
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Which SNP callers are suitable for QTL mapping in GBS experiments with low coverage?
SNP QTL-mapping GBS SNP caller low-coverage
3.2 years ago by rimgubaev ▴ 340
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0
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1.2k
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Answer: Answer: Which SNP callers are suitable for QTL mapping in GBS experiments with low cover
3.2 years ago by rimgubaev ▴ 340
2
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0
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1.6k
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Answer: Answer: QTL mapping by GBS
3.2 years ago by rimgubaev ▴ 340
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0
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4.9k
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Answer: Answer: GBS SNPs calling
3.2 years ago by rimgubaev ▴ 340
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0
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1.7k
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Answer: Answer: Best (GATK compatible) RadSeq/GBS pipeline in 2021
3.2 years ago by rimgubaev ▴ 340
2
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4
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2.3k
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How to add a individuals IDs to admixture output?
admixture population genetics
updated 2.3 years ago by • 0 • written 6.2 years ago by ▴ 340
3
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5
replies
4.8k
views
Could somebody suggest free pathway visualization tool for omics data from plants?
Vizualization Pathways RNA-Seq
updated 4.2 years ago by ▴ 440 • written 6.9 years ago by ▴ 340
0
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0
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808
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How to formally test the replicate consistency having genotype data?
SNP genetic variance replicates vcf consistency
4.2 years ago by rimgubaev ▴ 340
0
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0
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1.1k
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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
4.5 years ago by rimgubaev ▴ 340
0
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2
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1.4k
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What tools to use for genetic map construction or marker ordering using large SNP datasets?
GBS SNP Genetic map Marker ordering QTL
4.9 years ago by rimgubaev ▴ 340
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0
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1.1k
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Comment: C: How to calculate number of positions covered by at least 10 times in bam file?
5.1 years ago by rimgubaev ▴ 340
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1.1k
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Comment: C: How to calculate number of positions covered by at least 10 times in bam file?
5.1 years ago by rimgubaev ▴ 340
4
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4
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1.1k
views
How to calculate number of positions covered by at least 10 times in bam file?
coverage bam alignment bedtools awk
updated 5.1 years ago by 88k • written 5.1 years ago by ▴ 340
1
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0
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1.0k
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How to liftover SNPs between different assemblies from different databases?
SNP liftover ENSEMBL NCBI Assembly
updated 5.2 years ago by 20 • written 5.3 years ago by ▴ 340
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0
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28k
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Comment: C: intersect VCF files
5.3 years ago by rimgubaev ▴ 340
0
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2
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1.5k
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How to obtain an annotation for the list of NCBI's Gene ID?
NCBI GeneID annotation
5.3 years ago by rimgubaev ▴ 340
0
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0
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923
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Which option is better for variance component estimation in TASSEL?
TASSEL GWAS Variance P3D MLM
updated 5.3 years ago by 20 • written 5.4 years ago by ▴ 340
3
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5
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3.7k
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Tools to filter the heterozygous SNPs with biased allele depth (AD) values in vcf file.
vcf GATK heterozygous SNPs Allele depth AD
updated 4.2 years ago by 166k • written 5.3 years ago by ▴ 340
0
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0
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1.1k
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Heterozygous calls (SNPs) problem while working with inbred lines.
SNPs heterozygous GATK Sequencing errors vcf
5.3 years ago by rimgubaev ▴ 340
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0
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4.7k
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Comment: C: Using Gatk On Inbred Species - What To Do With The Heterozygous Calls?
5.4 years ago by rimgubaev ▴ 340
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1
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1.1k
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Comment: C: Is it ok to use median instead of mean for phenotype data in GWAS studies?
5.4 years ago by rimgubaev ▴ 340
0
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3
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1.1k
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Is it ok to use median instead of mean for phenotype data in GWAS studies?
GWAS association phenotype data
5.4 years ago by rimgubaev ▴ 340
0
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0
replies
908
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What is optimal distance to scan for genes near SNPs for pathway overrepresentation analysis?
pathway analysis pathways GWAS SnpEff SNP
5.5 years ago by rimgubaev ▴ 340
0
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0
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1.1k
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How to annotate only closest SNP using SnpEff?
SnpEff annotation SNP
5.5 years ago by rimgubaev ▴ 340
0
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0
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1.5k
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Tools and pipelines for bulk segregant analysis (BSA) in combination with genotyping-by-sequencing (GBS) techniques.
Association mapping BSA GBS
5.5 years ago by rimgubaev ▴ 340
0
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0
replies
651
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How many Individuals should I use in order to define haploblocks?
Haploblocks Population genetics Sample size LD
5.5 years ago by rimgubaev ▴ 340
0
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1
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1.2k
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Comment: C: How to select SNPs for haploblock identification after GWAS analysis?
5.5 years ago by rimgubaev ▴ 340
5
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3
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1.2k
views
How to select SNPs for haploblock identification after GWAS analysis?
GWAS Haploblocks SNP
updated 5.5 years ago by 89k • written 5.5 years ago by ▴ 340
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1
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7.9k
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Comment: C: How to make Q-Q plots for different models at a single chart using R?
5.5 years ago by rimgubaev ▴ 340
7
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6
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7.9k
views
How to make Q-Q plots for different models at a single chart using R?
GWAS qqman Q–Q plot model selection
updated 3.6 years ago by ▴ 160 • written 5.5 years ago by ▴ 340
3
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0
replies
5.5k
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Answer: A: How to add a custom chromosome labels in qqman R package?
5.5 years ago by rimgubaev ▴ 340
5
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2
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5.5k
views
How to add a custom chromosome labels in qqman R package?
qqman GWAS manhattan plot chromosome labels
5.5 years ago by rimgubaev ▴ 340
0
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0
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5.5k
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Comment: C: What suggestive line at manhattan plot usually stands for?
5.5 years ago by rimgubaev ▴ 340
1
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2
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5.5k
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What suggestive line at manhattan plot usually stands for?
GWAS Manhattan plot Multiple testing correction
5.5 years ago by rimgubaev ▴ 340
0
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0
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3.0k
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Comment: C: Haplotypes For Each Sample
5.5 years ago by rimgubaev ▴ 340
1
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1
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945
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Could someone recommend courses/workshops on plant quantitative genetics?
Plant Genomics GWAS QTL mapping courses workshops
5.6 years ago by rimgubaev ▴ 340
0
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2
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981
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Is there any command line or GUI software to find SSR microsatellites using pattern?
SSR microsatellites Hordeum vulgare
updated 5.6 years ago by 166k • written 5.6 years ago by ▴ 340
0
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0
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2.6k
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Comment: C: How to extract promoter sequences from a plant draft genome?
5.7 years ago by rimgubaev ▴ 340
2
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2
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2.6k
views
Comment: C: How to extract promoter sequences from a plant draft genome?
5.7 years ago by rimgubaev ▴ 340
0
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1
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1.9k
views
Why kinship is a random effect while population structure is a fixed effect in GWAS studies?
Kinship matrix Principle components GWAS MLM
5.7 years ago by rimgubaev ▴ 340
0
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0
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2.0k
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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
5.7 years ago by rimgubaev ▴ 340
3
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1
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28k
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Comment: C: intersect VCF files
5.7 years ago by rimgubaev ▴ 340
0
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0
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1.3k
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How to convert vcf to SPAGeDi input format?
SPAGeDi VCF Kinship
updated 5.7 years ago by 20 • written 5.9 years ago by ▴ 340
0
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0
replies
860
views
What does the exclamation mark (!) means in Haploview output?
Haploview haploblocks LD
5.8 years ago by rimgubaev ▴ 340
1
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0
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989
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Is it possible to assign haplotypes to individuals using haploview?
Haploview haplotype blocks LD vcf plink
5.8 years ago by rimgubaev ▴ 340
0
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0
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2.9k
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How to interpret Centred IBS kinship matrix produced by TASSEL?
Kinship Centered IBS TASSEL
5.9 years ago by rimgubaev ▴ 340
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