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503
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Answer: Answer: Sample size, GxE GWAS
4 months ago by rimgubaev ▴ 330
1
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0
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341
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Comment: Comment: Interpretation of results obtained in GWAS analysis using MLMM
4 months ago by rimgubaev ▴ 330
1
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2
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515
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Answer: Answer: Why don't my map files contain cM values?
4 months ago by rimgubaev ▴ 330
1
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0
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1.4k
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Comment: Comment: How to add a individuals IDs to admixture output?
15 months ago by rimgubaev ▴ 330
1
vote
1
reply
742
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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
15 months ago by rimgubaev ▴ 330
1
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0
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742
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Answer: Answer: Which SNP callers are suitable for QTL mapping in GBS experiments with low cover
15 months ago by rimgubaev ▴ 330
2
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0
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1.1k
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Answer: Answer: QTL mapping by GBS
15 months ago by rimgubaev ▴ 330
1
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0
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3.7k
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Answer: Answer: GBS SNPs calling
15 months ago by rimgubaev ▴ 330
0
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0
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950
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Answer: Answer: Best (GATK compatible) RadSeq/GBS pipeline in 2021
15 months ago by rimgubaev ▴ 330
2
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4
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1.4k
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How to add a individuals IDs to admixture output?
admixture population genetics
updated 4 months ago by • 0 • written 4.2 years ago by ▴ 330
3
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5
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3.7k
views
Could somebody suggest free pathway visualization tool for omics data from plants?
Vizualization Pathways RNA-Seq
updated 2.2 years ago by ▴ 430 • written 5.0 years ago by ▴ 330
0
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0
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449
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How to formally test the replicate consistency having genotype data?
SNP genetic variance replicates vcf consistency
2.3 years ago by rimgubaev ▴ 330
0
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0
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804
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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
2.6 years ago by rimgubaev ▴ 330
0
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2
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880
views
What tools to use for genetic map construction or marker ordering using large SNP datasets?
GBS SNP Genetic map Marker ordering QTL
3.0 years ago by rimgubaev ▴ 330
0
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0
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656
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Comment: C: How to calculate number of positions covered by at least 10 times in bam file?
3.1 years ago by rimgubaev ▴ 330
0
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0
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656
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Comment: C: How to calculate number of positions covered by at least 10 times in bam file?
3.1 years ago by rimgubaev ▴ 330
4
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4
replies
656
views
How to calculate number of positions covered by at least 10 times in bam file?
coverage bam alignment bedtools awk
updated 3.1 years ago by 72k • written 3.1 years ago by ▴ 330
1
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0
replies
713
views
How to liftover SNPs between different assemblies from different databases?
SNP liftover ENSEMBL NCBI Assembly
updated 3.2 years ago by 20 • written 3.3 years ago by ▴ 330
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0
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20k
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Comment: C: intersect VCF files
3.4 years ago by rimgubaev ▴ 330
0
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2
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1.0k
views
How to obtain an annotation for the list of NCBI's Gene ID?
NCBI GeneID annotation
3.4 years ago by rimgubaev ▴ 330
0
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0
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638
views
Which option is better for variance component estimation in TASSEL?
TASSEL GWAS Variance P3D MLM
updated 3.4 years ago by 20 • written 3.4 years ago by ▴ 330
3
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5
replies
2.4k
views
Tools to filter the heterozygous SNPs with biased allele depth (AD) values in vcf file.
vcf GATK heterozygous SNPs Allele depth AD
updated 2.2 years ago by 154k • written 3.4 years ago by ▴ 330
0
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0
replies
753
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Heterozygous calls (SNPs) problem while working with inbred lines.
SNPs heterozygous GATK Sequencing errors vcf
3.4 years ago by rimgubaev ▴ 330
0
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0
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4.0k
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Comment: C: Using Gatk On Inbred Species - What To Do With The Heterozygous Calls?
3.4 years ago by rimgubaev ▴ 330
0
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1
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557
views
Comment: C: Is it ok to use median instead of mean for phenotype data in GWAS studies?
3.4 years ago by rimgubaev ▴ 330
0
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3
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557
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Is it ok to use median instead of mean for phenotype data in GWAS studies?
GWAS association phenotype data
3.4 years ago by rimgubaev ▴ 330
0
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0
replies
606
views
What is optimal distance to scan for genes near SNPs for pathway overrepresentation analysis?
pathway analysis pathways GWAS SnpEff SNP
3.5 years ago by rimgubaev ▴ 330
0
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0
replies
826
views
How to annotate only closest SNP using SnpEff?
SnpEff annotation SNP
3.5 years ago by rimgubaev ▴ 330
0
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0
replies
996
views
Tools and pipelines for bulk segregant analysis (BSA) in combination with genotyping-by-sequencing (GBS) techniques.
Association mapping BSA GBS
3.5 years ago by rimgubaev ▴ 330
0
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0
replies
445
views
How many Individuals should I use in order to define haploblocks?
Haploblocks Population genetics Sample size LD
3.5 years ago by rimgubaev ▴ 330
0
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1
reply
718
views
Comment: C: How to select SNPs for haploblock identification after GWAS analysis?
3.5 years ago by rimgubaev ▴ 330
5
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3
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718
views
How to select SNPs for haploblock identification after GWAS analysis?
GWAS Haploblocks SNP
updated 3.5 years ago by 85k • written 3.5 years ago by ▴ 330
0
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1
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5.5k
views
Comment: C: How to make Q-Q plots for different models at a single chart using R?
3.5 years ago by rimgubaev ▴ 330
7
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6
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5.5k
views
How to make Q-Q plots for different models at a single chart using R?
GWAS qqman Q–Q plot model selection
updated 19 months ago by ▴ 150 • written 3.5 years ago by ▴ 330
3
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0
replies
3.9k
views
Answer: A: How to add a custom chromosome labels in qqman R package?
3.5 years ago by rimgubaev ▴ 330
5
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2
replies
3.9k
views
How to add a custom chromosome labels in qqman R package?
qqman GWAS manhattan plot chromosome labels
3.5 years ago by rimgubaev ▴ 330
0
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0
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3.7k
views
Comment: C: What suggestive line at manhattan plot usually stands for?
3.5 years ago by rimgubaev ▴ 330
1
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2
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3.7k
views
What suggestive line at manhattan plot usually stands for?
GWAS Manhattan plot Multiple testing correction
3.6 years ago by rimgubaev ▴ 330
0
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0
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2.4k
views
Comment: C: Haplotypes For Each Sample
3.6 years ago by rimgubaev ▴ 330
1
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1
reply
688
views
Could someone recommend courses/workshops on plant quantitative genetics?
Plant Genomics GWAS QTL mapping courses workshops
3.6 years ago by rimgubaev ▴ 330
0
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2
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640
views
Is there any command line or GUI software to find SSR microsatellites using pattern?
SSR microsatellites Hordeum vulgare
updated 3.7 years ago by 154k • written 3.7 years ago by ▴ 330
0
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0
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1.6k
views
Comment: C: How to extract promoter sequences from a plant draft genome?
3.7 years ago by rimgubaev ▴ 330
2
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2
replies
1.6k
views
Comment: C: How to extract promoter sequences from a plant draft genome?
3.7 years ago by rimgubaev ▴ 330
0
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1
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1.4k
views
Why kinship is a random effect while population structure is a fixed effect in GWAS studies?
Kinship matrix Principle components GWAS MLM
3.7 years ago by rimgubaev ▴ 330
0
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0
replies
1.5k
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
3.7 years ago by rimgubaev ▴ 330
3
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1
reply
20k
views
Comment: C: intersect VCF files
3.7 years ago by rimgubaev ▴ 330
0
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0
replies
869
views
How to convert vcf to SPAGeDi input format?
SPAGeDi VCF Kinship
updated 3.7 years ago by 20 • written 3.9 years ago by ▴ 330
0
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0
replies
585
views
What does the exclamation mark (!) means in Haploview output?
Haploview haploblocks LD
3.9 years ago by rimgubaev ▴ 330
0
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0
replies
667
views
Is it possible to assign haplotypes to individuals using haploview?
Haploview haplotype blocks LD vcf plink
3.9 years ago by rimgubaev ▴ 330
0
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0
replies
2.2k
views
How to interpret Centred IBS kinship matrix produced by TASSEL?
Kinship Centered IBS TASSEL
3.9 years ago by rimgubaev ▴ 330
104 results • Page 1 of 3
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