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Comment: Comment: How to add a individuals IDs to admixture output?
5 months ago by rimgubaev ▴ 280
1
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1
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594
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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
5 months ago by rimgubaev ▴ 280
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0
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Answer: Answer: Which SNP callers are suitable for QTL mapping in GBS experiments with low cover
5 months ago by rimgubaev ▴ 280
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0
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765
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Answer: Answer: QTL mapping by GBS
5 months ago by rimgubaev ▴ 280
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3.3k
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Answer: Answer: GBS SNPs calling
5 months ago by rimgubaev ▴ 280
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671
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Answer: Answer: Best (GATK compatible) RadSeq/GBS pipeline in 2021
5 months ago by rimgubaev ▴ 280
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3
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1.0k
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How to add a individuals IDs to admixture output?
admixture population genetics
5 months ago by rimgubaev ▴ 280
3
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5
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3.3k
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Could somebody suggest free pathway visualization tool for omics data from plants?
Vizualization Pathways RNA-Seq
updated 16 months ago by ▴ 430 • written 4.1 years ago by ▴ 280
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321
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How to formally test the replicate consistency having genotype data?
SNP genetic variance replicates vcf consistency
17 months ago by rimgubaev ▴ 280
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0
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668
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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
21 months ago by rimgubaev ▴ 280
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2
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701
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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
2.2 years ago by rimgubaev ▴ 280
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466
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Comment: C: How to calculate number of positions covered by at least 10 times in bam file?
2.3 years ago by rimgubaev ▴ 280
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466
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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
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4
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466
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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 64k • written 2.3 years ago by ▴ 280
1
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567
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How to liftover SNPs between different assemblies from different databases?
SNP liftover ENSEMBL NCBI Assembly
updated 2.4 years ago by 20 • written 2.5 years ago by ▴ 280
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16k
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Comment: C: intersect VCF files
2.5 years ago by rimgubaev ▴ 280
0
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2
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877
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How to obtain an annotation for the list of NCBI's Gene ID?
NCBI GeneID annotation
2.6 years ago by rimgubaev ▴ 280
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0
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534
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Which option is better for variance component estimation in TASSEL?
TASSEL GWAS Variance P3D MLM
updated 2.6 years ago by 20 • written 2.6 years ago by ▴ 280
3
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5
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1.9k
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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 16 months ago by 147k • written 2.6 years ago by ▴ 280
0
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0
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624
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Heterozygous calls (SNPs) problem while working with inbred lines.
SNPs heterozygous GATK Sequencing errors vcf
2.6 years ago by rimgubaev ▴ 280
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0
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3.8k
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Comment: C: Using Gatk On Inbred Species - What To Do With The Heterozygous Calls?
2.6 years ago by rimgubaev ▴ 280
0
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1
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411
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Comment: C: Is it ok to use median instead of mean for phenotype data in GWAS studies?
2.6 years ago by rimgubaev ▴ 280
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3
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411
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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
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0
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487
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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
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0
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694
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How to annotate only closest SNP using SnpEff?
SnpEff annotation SNP
2.7 years ago by rimgubaev ▴ 280
0
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0
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803
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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
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0
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370
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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
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1
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545
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Comment: C: How to select SNPs for haploblock identification after GWAS analysis?
2.7 years ago by rimgubaev ▴ 280
5
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3
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545
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How to select SNPs for haploblock identification after GWAS analysis?
GWAS Haploblocks SNP
updated 2.7 years ago by 82k • written 2.7 years ago by ▴ 280
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1
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4.4k
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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
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6
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4.4k
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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 ▴ 130 • written 2.7 years ago by ▴ 280
3
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0
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3.1k
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Answer: A: How to add a custom chromosome labels in qqman R package?
2.7 years ago by rimgubaev ▴ 280
5
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2
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3.1k
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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
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0
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2.9k
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Comment: C: What suggestive line at manhattan plot usually stands for?
2.7 years ago by rimgubaev ▴ 280
1
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2
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2.9k
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What suggestive line at manhattan plot usually stands for?
GWAS Manhattan plot Multiple testing correction
2.7 years ago by rimgubaev ▴ 280
0
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0
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2.3k
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Comment: C: Haplotypes For Each Sample
2.7 years ago by rimgubaev ▴ 280
1
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1
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589
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Could someone recommend courses/workshops on plant quantitative genetics?
Plant Genomics GWAS QTL mapping courses workshops
2.8 years ago by rimgubaev ▴ 280
0
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2
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533
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Is there any command line or GUI software to find SSR microsatellites using pattern?
SSR microsatellites Hordeum vulgare
updated 2.8 years ago by 147k • written 2.8 years ago by ▴ 280
0
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0
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1.3k
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Comment: C: How to extract promoter sequences from a plant draft genome?
2.9 years ago by rimgubaev ▴ 280
2
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2
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1.3k
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Comment: C: How to extract promoter sequences from a plant draft genome?
2.9 years ago by rimgubaev ▴ 280
0
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1
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1.2k
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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
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0
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1.3k
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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
2.9 years ago by rimgubaev ▴ 280
3
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1
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16k
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Comment: C: intersect VCF files
2.9 years ago by rimgubaev ▴ 280
0
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0
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735
views
How to convert vcf to SPAGeDi input format?
SPAGeDi VCF Kinship
updated 2.9 years ago by 20 • written 3.1 years ago by ▴ 280
0
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0
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507
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What does the exclamation mark (!) means in Haploview output?
Haploview haploblocks LD
3.0 years ago by rimgubaev ▴ 280
0
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0
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533
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Is it possible to assign haplotypes to individuals using haploview?
Haploview haplotype blocks LD vcf plink
3.0 years ago by rimgubaev ▴ 280
0
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0
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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
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0
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601
views
Comment: C: Is it ok to use genotype replicates for association studies?
3.1 years ago by rimgubaev ▴ 280
1
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3
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601
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Is it ok to use genotype replicates for association studies?
GWAS permutation test TASSEL
3.1 years ago by rimgubaev ▴ 280
0
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1
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830
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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
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