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909
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Answer: Answer: Sample size, GxE GWAS
15 months ago by rimgubaev ▴ 330
1
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0
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520
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Comment: Comment: Interpretation of results obtained in GWAS analysis using MLMM
15 months ago by rimgubaev ▴ 330
1
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2
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1.1k
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Answer: Answer: Why don't my map files contain cM values?
15 months ago by rimgubaev ▴ 330
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0
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1.8k
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Comment: Comment: How to add a individuals IDs to admixture output?
2.2 years ago by rimgubaev ▴ 330
1
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1
reply
922
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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
2.2 years ago by rimgubaev ▴ 330
1
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0
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922
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Answer: Answer: Which SNP callers are suitable for QTL mapping in GBS experiments with low cover
2.2 years ago by rimgubaev ▴ 330
2
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0
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1.3k
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Answer: Answer: QTL mapping by GBS
2.2 years ago by rimgubaev ▴ 330
1
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0
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4.2k
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Answer: Answer: GBS SNPs calling
2.2 years ago by rimgubaev ▴ 330
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0
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1.3k
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Answer: Answer: Best (GATK compatible) RadSeq/GBS pipeline in 2021
2.2 years ago by rimgubaev ▴ 330
2
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4
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1.8k
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How to add a individuals IDs to admixture output?
admixture population genetics
updated 15 months ago by • 0 • written 5.1 years ago by ▴ 330
3
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5
replies
4.2k
views
Could somebody suggest free pathway visualization tool for omics data from plants?
Vizualization Pathways RNA-Seq
updated 3.1 years ago by ▴ 430 • written 5.9 years ago by ▴ 330
0
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0
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582
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How to formally test the replicate consistency having genotype data?
SNP genetic variance replicates vcf consistency
3.2 years ago by rimgubaev ▴ 330
0
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0
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973
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
3.5 years ago by rimgubaev ▴ 330
0
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2
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1.1k
views
What tools to use for genetic map construction or marker ordering using large SNP datasets?
GBS SNP Genetic map Marker ordering QTL
3.9 years ago by rimgubaev ▴ 330
0
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0
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843
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Comment: C: How to calculate number of positions covered by at least 10 times in bam file?
4.0 years ago by rimgubaev ▴ 330
0
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0
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843
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Comment: C: How to calculate number of positions covered by at least 10 times in bam file?
4.0 years ago by rimgubaev ▴ 330
4
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4
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843
views
How to calculate number of positions covered by at least 10 times in bam file?
coverage bam alignment bedtools awk
updated 4.0 years ago by 82k • written 4.0 years ago by ▴ 330
1
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0
replies
862
views
How to liftover SNPs between different assemblies from different databases?
SNP liftover ENSEMBL NCBI Assembly
updated 4.1 years ago by 20 • written 4.2 years ago by ▴ 330
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0
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24k
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Comment: C: intersect VCF files
4.3 years ago by rimgubaev ▴ 330
0
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2
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1.2k
views
How to obtain an annotation for the list of NCBI's Gene ID?
NCBI GeneID annotation
4.3 years ago by rimgubaev ▴ 330
0
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0
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762
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Which option is better for variance component estimation in TASSEL?
TASSEL GWAS Variance P3D MLM
updated 4.3 years ago by 20 • written 4.3 years ago by ▴ 330
3
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5
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3.0k
views
Tools to filter the heterozygous SNPs with biased allele depth (AD) values in vcf file.
vcf GATK heterozygous SNPs Allele depth AD
updated 3.1 years ago by 161k • written 4.3 years ago by ▴ 330
0
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0
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879
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Heterozygous calls (SNPs) problem while working with inbred lines.
SNPs heterozygous GATK Sequencing errors vcf
4.3 years ago by rimgubaev ▴ 330
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0
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4.3k
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Comment: C: Using Gatk On Inbred Species - What To Do With The Heterozygous Calls?
4.3 years ago by rimgubaev ▴ 330
0
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1
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754
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Comment: C: Is it ok to use median instead of mean for phenotype data in GWAS studies?
4.3 years ago by rimgubaev ▴ 330
0
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3
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754
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Is it ok to use median instead of mean for phenotype data in GWAS studies?
GWAS association phenotype data
4.3 years ago by rimgubaev ▴ 330
0
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0
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733
views
What is optimal distance to scan for genes near SNPs for pathway overrepresentation analysis?
pathway analysis pathways GWAS SnpEff SNP
4.4 years ago by rimgubaev ▴ 330
0
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0
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962
views
How to annotate only closest SNP using SnpEff?
SnpEff annotation SNP
4.4 years ago by rimgubaev ▴ 330
0
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0
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1.2k
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Tools and pipelines for bulk segregant analysis (BSA) in combination with genotyping-by-sequencing (GBS) techniques.
Association mapping BSA GBS
4.4 years ago by rimgubaev ▴ 330
0
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0
replies
543
views
How many Individuals should I use in order to define haploblocks?
Haploblocks Population genetics Sample size LD
4.4 years ago by rimgubaev ▴ 330
0
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1
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937
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Comment: C: How to select SNPs for haploblock identification after GWAS analysis?
4.4 years ago by rimgubaev ▴ 330
5
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3
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937
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How to select SNPs for haploblock identification after GWAS analysis?
GWAS Haploblocks SNP
updated 4.4 years ago by 87k • written 4.4 years ago by ▴ 330
0
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1
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6.9k
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Comment: C: How to make Q-Q plots for different models at a single chart using R?
4.4 years ago by rimgubaev ▴ 330
7
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6
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6.9k
views
How to make Q-Q plots for different models at a single chart using R?
GWAS qqman Q–Q plot model selection
updated 2.5 years ago by ▴ 160 • written 4.4 years ago by ▴ 330
3
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0
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4.7k
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Answer: A: How to add a custom chromosome labels in qqman R package?
4.4 years ago by rimgubaev ▴ 330
5
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2
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4.7k
views
How to add a custom chromosome labels in qqman R package?
qqman GWAS manhattan plot chromosome labels
4.4 years ago by rimgubaev ▴ 330
0
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0
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4.4k
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Comment: C: What suggestive line at manhattan plot usually stands for?
4.5 years ago by rimgubaev ▴ 330
1
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2
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4.4k
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What suggestive line at manhattan plot usually stands for?
GWAS Manhattan plot Multiple testing correction
4.5 years ago by rimgubaev ▴ 330
0
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0
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2.7k
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Comment: C: Haplotypes For Each Sample
4.5 years ago by rimgubaev ▴ 330
1
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1
reply
809
views
Could someone recommend courses/workshops on plant quantitative genetics?
Plant Genomics GWAS QTL mapping courses workshops
4.5 years ago by rimgubaev ▴ 330
0
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2
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777
views
Is there any command line or GUI software to find SSR microsatellites using pattern?
SSR microsatellites Hordeum vulgare
updated 4.6 years ago by 161k • written 4.6 years ago by ▴ 330
0
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0
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2.0k
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Comment: C: How to extract promoter sequences from a plant draft genome?
4.6 years ago by rimgubaev ▴ 330
2
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2
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2.0k
views
Comment: C: How to extract promoter sequences from a plant draft genome?
4.6 years ago by rimgubaev ▴ 330
0
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1
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1.6k
views
Why kinship is a random effect while population structure is a fixed effect in GWAS studies?
Kinship matrix Principle components GWAS MLM
4.6 years ago by rimgubaev ▴ 330
0
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0
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1.7k
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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
4.6 years ago by rimgubaev ▴ 330
3
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1
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24k
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Comment: C: intersect VCF files
4.6 years ago by rimgubaev ▴ 330
0
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0
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1.1k
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How to convert vcf to SPAGeDi input format?
SPAGeDi VCF Kinship
updated 4.7 years ago by 20 • written 4.8 years ago by ▴ 330
0
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0
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708
views
What does the exclamation mark (!) means in Haploview output?
Haploview haploblocks LD
4.8 years ago by rimgubaev ▴ 330
0
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0
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812
views
Is it possible to assign haplotypes to individuals using haploview?
Haploview haplotype blocks LD vcf plink
4.8 years ago by rimgubaev ▴ 330
0
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0
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2.5k
views
How to interpret Centred IBS kinship matrix produced by TASSEL?
Kinship Centered IBS TASSEL
4.8 years ago by rimgubaev ▴ 330
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