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2
votes
5
replies
2.7k
views
Could somebody suggest free pathway visualization tool for omics data from plants?
Vizualization Pathways RNA-Seq
updated 7 months ago by ▴ 410 • written 3.4 years ago by ▴ 270
0
votes
0
replies
187
views
How to formally test the replicate consistency having genotype data?
SNP genetic variance replicates vcf consistency
8 months ago by rimgubaev ▴ 270
0
votes
0
replies
441
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
11 months ago by rimgubaev ▴ 270
0
votes
2
replies
473
views
What tools to use for genetic map construction or marker ordering using large SNP datasets?
GBS SNP Genetic map Marker ordering QTL
16 months ago by rimgubaev ▴ 270
0
votes
0
replies
304
views
Which SNP callers are suitable for QTL mapping in GBS experiments with low coverage?
SNP QTL-mapping GBS SNP caller low-coverage
18 months ago by rimgubaev ▴ 270
0
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0
replies
302
views
Comment: C: How to calculate number of positions covered by at least 10 times in bam file?
18 months ago by rimgubaev ▴ 270
0
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0
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302
views
Comment: C: How to calculate number of positions covered by at least 10 times in bam file?
18 months ago by rimgubaev ▴ 270
4
votes
4
replies
302
views
How to calculate number of positions covered by at least 10 times in bam file?
coverage bam alignment bedtools awk
updated 18 months ago by 55k • written 18 months ago by ▴ 270
1
vote
0
replies
412
views
How to liftover SNPs between different assemblies from different databases?
SNP liftover ENSEMBL NCBI Assembly
updated 19 months ago by 20 • written 21 months ago by ▴ 270
0
votes
0
replies
12k
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Comment: C: intersect VCF files
21 months ago by rimgubaev ▴ 270
0
votes
2
replies
661
views
How to obtain an annotation for the list of NCBI's Gene ID?
NCBI GeneID annotation
21 months ago by rimgubaev ▴ 270
0
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0
replies
402
views
Which option is better for variance component estimation in TASSEL?
TASSEL GWAS Variance P3D MLM
updated 21 months ago by 20 • written 21 months ago by ▴ 270
3
votes
5
replies
1.3k
views
Tools to filter the heterozygous SNPs with biased allele depth (AD) values in vcf file.
vcf GATK heterozygous SNPs Allele depth AD
updated 7 months ago by 139k • written 21 months ago by ▴ 270
0
votes
0
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437
views
Heterozygous calls (SNPs) problem while working with inbred lines.
SNPs heterozygous GATK Sequencing errors vcf
21 months ago by rimgubaev ▴ 270
0
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0
replies
3.6k
views
Comment: C: Using Gatk On Inbred Species - What To Do With The Heterozygous Calls?
21 months ago by rimgubaev ▴ 270
0
votes
1
reply
278
views
Comment: C: Is it ok to use median instead of mean for phenotype data in GWAS studies?
21 months ago by rimgubaev ▴ 270
0
votes
3
replies
278
views
Is it ok to use median instead of mean for phenotype data in GWAS studies?
GWAS association phenotype data
21 months ago by rimgubaev ▴ 270
0
votes
0
replies
337
views
What is optimal distance to scan for genes near SNPs for pathway overrepresentation analysis?
pathway analysis pathways GWAS SnpEff SNP
22 months ago by rimgubaev ▴ 270
0
votes
0
replies
541
views
How to annotate only closest SNP using SnpEff?
SnpEff annotation SNP
22 months ago by rimgubaev ▴ 270
0
votes
0
replies
534
views
Tools and pipelines for bulk segregant analysis (BSA) in combination with genotyping-by-sequencing (GBS) techniques.
Association mapping BSA GBS
23 months ago by rimgubaev ▴ 270
0
votes
0
replies
251
views
How many Individuals should I use in order to define haploblocks?
Haploblocks Population genetics Sample size LD
23 months ago by rimgubaev ▴ 270
0
votes
1
reply
412
views
Comment: C: How to select SNPs for haploblock identification after GWAS analysis?
23 months ago by rimgubaev ▴ 270
5
votes
3
replies
412
views
How to select SNPs for haploblock identification after GWAS analysis?
GWAS Haploblocks SNP
updated 23 months ago by 78k • written 23 months ago by ▴ 270
0
votes
1
reply
3.1k
views
Comment: C: How to make Q-Q plots for different models at a single chart using R?
23 months ago by rimgubaev ▴ 270
7
votes
6
replies
3.1k
views
How to make Q-Q plots for different models at a single chart using R?
GWAS qqman Q–Q plot model selection
updated 1 day ago by ▴ 120 • written 23 months ago by ▴ 270
5
votes
2
replies
2.2k
views
How to add a custom chromosome labels in qqman R package?
qqman GWAS manhattan plot chromosome labels
23 months ago by rimgubaev ▴ 270
3
votes
0
replies
2.2k
views
Answer: A: How to add a custom chromosome labels in qqman R package?
23 months ago by rimgubaev ▴ 270
0
votes
0
replies
1.9k
views
Comment: C: What suggestive line at manhattan plot usually stands for?
23 months ago by rimgubaev ▴ 270
1
vote
2
replies
1.9k
views
What suggestive line at manhattan plot usually stands for?
GWAS Manhattan plot Multiple testing correction
23 months ago by rimgubaev ▴ 270
0
votes
0
replies
2.1k
views
Comment: C: Haplotypes For Each Sample
23 months ago by rimgubaev ▴ 270
1
vote
1
reply
441
views
Could someone recommend courses/workshops on plant quantitative genetics?
Plant Genomics GWAS QTL mapping courses workshops
2.0 years ago by rimgubaev ▴ 270
0
votes
2
replies
399
views
Is there any command line or GUI software to find SSR microsatellites using pattern?
SSR microsatellites Hordeum vulgare
updated 2.1 years ago by 139k • written 2.1 years ago by ▴ 270
0
votes
0
replies
923
views
Comment: C: How to extract promoter sequences from a plant draft genome?
2.1 years ago by rimgubaev ▴ 270
2
votes
2
replies
923
views
Comment: C: How to extract promoter sequences from a plant draft genome?
2.1 years ago by rimgubaev ▴ 270
0
votes
1
reply
904
views
Why kinship is a random effect while population structure is a fixed effect in GWAS studies?
Kinship matrix Principle components GWAS MLM
2.1 years ago by rimgubaev ▴ 270
0
votes
0
replies
979
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
2.1 years ago by rimgubaev ▴ 270
3
votes
1
reply
12k
views
Comment: C: intersect VCF files
2.1 years ago by rimgubaev ▴ 270
0
votes
0
replies
561
views
How to convert vcf to SPAGeDi input format?
SPAGeDi VCF Kinship
updated 2.2 years ago by 20 • written 2.3 years ago by ▴ 270
0
votes
0
replies
388
views
What does the exclamation mark (!) means in Haploview output?
Haploview haploblocks LD
2.3 years ago by rimgubaev ▴ 270
0
votes
0
replies
384
views
Is it possible to assign haplotypes to individuals using haploview?
Haploview haplotype blocks LD vcf plink
2.3 years ago by rimgubaev ▴ 270
0
votes
0
replies
1.5k
views
How to interpret Centred IBS kinship matrix produced by TASSEL?
Kinship Centered IBS TASSEL
2.3 years ago by rimgubaev ▴ 270
0
votes
0
replies
451
views
Comment: C: Is it ok to use genotype replicates for association studies?
2.3 years ago by rimgubaev ▴ 270
1
vote
3
replies
451
views
Is it ok to use genotype replicates for association studies?
GWAS permutation test TASSEL
2.3 years ago by rimgubaev ▴ 270
0
votes
1
reply
588
views
Comment: C: How to make association studies using haplotype (LD) blocks instead of SNPs?
2.3 years ago by rimgubaev ▴ 270
2
votes
3
replies
588
views
How to make association studies using haplotype (LD) blocks instead of SNPs?
LD SNPs Haplotype GWAS
2.3 years ago by rimgubaev ▴ 270
2
votes
0
replies
887
views
Which test is applied in order to generate p-values in TASSEL when using Mixed Linear Model?
TASSEL GWAS statistical test
updated 2.4 years ago by 20 • written 2.5 years ago by ▴ 270
4
votes
1
reply
1.8k
views
How to interpret slash (/) and vertical pipe (|) in GATK's vcf output?
GATK VCF formatting
updated 2.4 years ago by 33k • written 2.4 years ago by ▴ 270
0
votes
0
replies
566
views
Has anyone dealt with "Specified element is out of bounds" error produced by TASSEL?
GWAS TASSEL MLM Mixed linear model
2.4 years ago by rimgubaev ▴ 270
0
votes
1
reply
1.0k
views
Comment: A: Convert RefseqID to EntrezID
2.5 years ago by rimgubaev ▴ 270
1
vote
1
reply
1.2k
views
Which R packages are fit for calculating distances and make phylogenetic trees from VCF files?
VCF RNA-Seq Phylogeny populational genetics trees
2.5 years ago by rimgubaev ▴ 270
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