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915
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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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523
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Comment: Comment: Interpretation of results obtained in GWAS analysis using MLMM
16 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?
16 months ago by rimgubaev ▴ 330
1
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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
927
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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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927
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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
0
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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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588
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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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851
views
Comment: C: How to calculate number of positions covered by at least 10 times in bam file?
4.1 years ago by rimgubaev ▴ 330
0
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0
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851
views
Comment: C: How to calculate number of positions covered by at least 10 times in bam file?
4.1 years ago by rimgubaev ▴ 330
4
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4
replies
851
views
How to calculate number of positions covered by at least 10 times in bam file?
coverage bam alignment bedtools awk
updated 4.1 years ago by 82k • written 4.1 years ago by ▴ 330
1
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0
replies
864
views
How to liftover SNPs between different assemblies from different databases?
SNP liftover ENSEMBL NCBI Assembly
updated 4.1 years ago by 20 • written 4.3 years ago by ▴ 330
0
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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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765
views
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
replies
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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880
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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
0
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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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757
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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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757
views
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
replies
734
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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964
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
replies
1.2k
views
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
545
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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941
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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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941
views
How to select SNPs for haploblock identification after GWAS analysis?
GWAS Haploblocks SNP
updated 4.4 years ago by 87k • written 4.5 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?
4.5 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 4.5 years ago by ▴ 330
3
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0
replies
4.7k
views
Answer: A: How to add a custom chromosome labels in qqman R package?
4.5 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
4.5 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
views
Comment: C: Haplotypes For Each Sample
4.5 years ago by rimgubaev ▴ 330
1
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1
reply
813
views
Could someone recommend courses/workshops on plant quantitative genetics?
Plant Genomics GWAS QTL mapping courses workshops
4.6 years ago by rimgubaev ▴ 330
0
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2
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782
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
replies
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
reply
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
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
4.7 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
4.7 years ago by rimgubaev ▴ 330
0
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0
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1.1k
views
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
replies
711
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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814
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
104 results • Page 1 of 3
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