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1
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614
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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
6 months ago by rimgubaev ▴ 280
2
votes
3
replies
1.1k
views
How to add a individuals IDs to admixture output?
admixture population genetics
6 months ago by rimgubaev ▴ 280
3
votes
5
replies
3.3k
views
Could somebody suggest free pathway visualization tool for omics data from plants?
Vizualization Pathways RNA-Seq
updated 18 months ago by ▴ 430 • written 4.3 years ago by ▴ 280
0
votes
0
replies
345
views
How to formally test the replicate consistency having genotype data?
SNP genetic variance replicates vcf consistency
19 months ago by rimgubaev ▴ 280
0
votes
0
replies
689
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
23 months ago by rimgubaev ▴ 280
0
votes
2
replies
723
views
What tools to use for genetic map construction or marker ordering using large SNP datasets?
GBS SNP Genetic map Marker ordering QTL
2.3 years ago by rimgubaev ▴ 280
4
votes
4
replies
506
views
How to calculate number of positions covered by at least 10 times in bam file?
coverage bam alignment bedtools awk
updated 2.5 years ago by 65k • written 2.5 years ago by ▴ 280
1
vote
0
replies
589
views
How to liftover SNPs between different assemblies from different databases?
SNP liftover ENSEMBL NCBI Assembly
updated 2.5 years ago by 20 • written 2.6 years ago by ▴ 280
0
votes
2
replies
904
views
How to obtain an annotation for the list of NCBI's Gene ID?
NCBI GeneID annotation
2.7 years ago by rimgubaev ▴ 280
0
votes
0
replies
551
views
Which option is better for variance component estimation in TASSEL?
TASSEL GWAS Variance P3D MLM
updated 2.7 years ago by 20 • written 2.7 years ago by ▴ 280
3
votes
5
replies
2.0k
views
Tools to filter the heterozygous SNPs with biased allele depth (AD) values in vcf file.
vcf GATK heterozygous SNPs Allele depth AD
updated 18 months ago by 149k • written 2.7 years ago by ▴ 280
0
votes
0
replies
646
views
Heterozygous calls (SNPs) problem while working with inbred lines.
SNPs heterozygous GATK Sequencing errors vcf
2.7 years ago by rimgubaev ▴ 280
0
votes
3
replies
429
views
Is it ok to use median instead of mean for phenotype data in GWAS studies?
GWAS association phenotype data
2.7 years ago by rimgubaev ▴ 280
0
votes
0
replies
506
views
What is optimal distance to scan for genes near SNPs for pathway overrepresentation analysis?
pathway analysis pathways GWAS SnpEff SNP
2.8 years ago by rimgubaev ▴ 280
0
votes
0
replies
707
views
How to annotate only closest SNP using SnpEff?
SnpEff annotation SNP
2.8 years ago by rimgubaev ▴ 280
0
votes
0
replies
827
views
Tools and pipelines for bulk segregant analysis (BSA) in combination with genotyping-by-sequencing (GBS) techniques.
Association mapping BSA GBS
2.8 years ago by rimgubaev ▴ 280
0
votes
0
replies
382
views
How many Individuals should I use in order to define haploblocks?
Haploblocks Population genetics Sample size LD
2.8 years ago by rimgubaev ▴ 280
5
votes
3
replies
570
views
How to select SNPs for haploblock identification after GWAS analysis?
GWAS Haploblocks SNP
updated 2.8 years ago by 83k • written 2.8 years ago by ▴ 280
7
votes
6
replies
4.6k
views
How to make Q-Q plots for different models at a single chart using R?
GWAS qqman Q–Q plot model selection
updated 11 months ago by ▴ 130 • written 2.8 years ago by ▴ 280
5
votes
2
replies
3.3k
views
How to add a custom chromosome labels in qqman R package?
qqman GWAS manhattan plot chromosome labels
2.8 years ago by rimgubaev ▴ 280
1
vote
2
replies
3.0k
views
What suggestive line at manhattan plot usually stands for?
GWAS Manhattan plot Multiple testing correction
2.9 years ago by rimgubaev ▴ 280
1
vote
1
reply
607
views
Could someone recommend courses/workshops on plant quantitative genetics?
Plant Genomics GWAS QTL mapping courses workshops
2.9 years ago by rimgubaev ▴ 280
0
votes
2
replies
549
views
Is there any command line or GUI software to find SSR microsatellites using pattern?
SSR microsatellites Hordeum vulgare
updated 3.0 years ago by 149k • written 3.0 years ago by ▴ 280
0
votes
1
reply
1.2k
views
Why kinship is a random effect while population structure is a fixed effect in GWAS studies?
Kinship matrix Principle components GWAS MLM
3.0 years ago by rimgubaev ▴ 280
0
votes
0
replies
1.3k
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
3.0 years ago by rimgubaev ▴ 280
0
votes
0
replies
758
views
How to convert vcf to SPAGeDi input format?
SPAGeDi VCF Kinship
updated 3.1 years ago by 20 • written 3.2 years ago by ▴ 280
0
votes
0
replies
518
views
What does the exclamation mark (!) means in Haploview output?
Haploview haploblocks LD
3.2 years ago by rimgubaev ▴ 280
0
votes
0
replies
553
views
Is it possible to assign haplotypes to individuals using haploview?
Haploview haplotype blocks LD vcf plink
3.2 years ago by rimgubaev ▴ 280
0
votes
0
replies
1.9k
views
How to interpret Centred IBS kinship matrix produced by TASSEL?
Kinship Centered IBS TASSEL
3.2 years ago by rimgubaev ▴ 280
1
vote
3
replies
612
views
Is it ok to use genotype replicates for association studies?
GWAS permutation test TASSEL
3.2 years ago by rimgubaev ▴ 280
2
votes
3
replies
854
views
How to make association studies using haplotype (LD) blocks instead of SNPs?
LD SNPs Haplotype GWAS
3.3 years ago by rimgubaev ▴ 280
2
votes
0
replies
1.1k
views
Which test is applied in order to generate p-values in TASSEL when using Mixed Linear Model?
TASSEL GWAS statistical test
updated 3.3 years ago by 20 • written 3.4 years ago by ▴ 280
4
votes
1
reply
2.6k
views
How to interpret slash (/) and vertical pipe (|) in GATK's vcf output?
GATK VCF formatting
updated 3.3 years ago by 34k • written 3.3 years ago by ▴ 280
0
votes
0
replies
732
views
Has anyone dealt with "Specified element is out of bounds" error produced by TASSEL?
GWAS TASSEL MLM Mixed linear model
3.3 years ago by rimgubaev ▴ 280
1
vote
1
reply
1.6k
views
Which R packages are fit for calculating distances and make phylogenetic trees from VCF files?
VCF RNA-Seq Phylogeny populational genetics trees
3.4 years ago by rimgubaev ▴ 280
0
votes
0
replies
666
views
Can I build a phylgenetic tree using SNPs obtained by differen techniques?
GBS Population genetics array SNP
3.4 years ago by rimgubaev ▴ 280
2
votes
3
replies
1.9k
views
Why switch negative values in kinship matrix to zeros?
kinship population genetics TASSEL SPAGEDI
updated 3.4 years ago by 9.3k • written 3.4 years ago by ▴ 280
18
votes
7
replies
1.7k
views
How to merge multiple fastq file using table?
fastq cat bash
3.4 years ago by rimgubaev ▴ 280
1
vote
5
replies
3.1k
views
How to work with fasta files and make phylogenetics in R?
populational genetics R ape phangorn VCF
3.4 years ago by rimgubaev ▴ 280
0
votes
0
replies
652
views
Homozygous and heterozygous variants in Tassel5 output, what are they?
tassel SNP
3.5 years ago by rimgubaev ▴ 280
2
votes
7
replies
2.9k
views
How to build a phylogenetic tree using fasta obtained from VCF file?
Population genetics VCF MEGA
updated 17 months ago by ▴ 50 • written 3.5 years ago by ▴ 280
1
vote
3
replies
747
views
Structure produces no result
Structure Population genetics
3.5 years ago by rimgubaev ▴ 280
3
votes
8
replies
2.0k
views
How to make interval list for GBS sequencing?
GBS GATK4
3.5 years ago by rimgubaev ▴ 280
0
votes
1
reply
1.4k
views
What does LnP(D) per clusters K plot means?
GWAS Population genetics
3.7 years ago by rimgubaev ▴ 280
9
votes
3
replies
3.6k
views
Is it possible to make a PCA plot for samples using TPM exprssion values in R?
RNA-Seq PCA TPM
updated 4.0 years ago by 6.4k • written 4.0 years ago by ▴ 280
10
votes
7
replies
6.4k
views
Why volcano plot has no points in the middle of plot?
RNA-Seq Volcano plot
updated 4.1 years ago by 46k • written 4.1 years ago by ▴ 280
7
votes
3
replies
1.3k
views
What is wrong with NCBI's gff file?
GFF
4.1 years ago by rimgubaev ▴ 280
3
votes
2
replies
984
views
Are there some ways to extract information in tabular format from text with regular pattern?
text mining promoter analysis NsiteM
4.1 years ago by rimgubaev ▴ 280
7
votes
4
replies
3.7k
views
How to extract all promoter regions in multi-fasta format from genome using GFF?
promoter genome gff fasta
4.2 years ago by rimgubaev ▴ 280
0
votes
2
replies
919
views
How to search cis-regulatory elemens using promoter multifasta from non-model plant?
cis-regulatory element multifasta non-model plant
4.3 years ago by rimgubaev ▴ 280
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