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1
vote
3
replies
6.9k
views
MrBayes chains converged, how to stop early?
phylogeny bayesian mrbayes
updated 19 months ago by • 0 • written 9.0 years ago by ★ 2.6k
0
votes
2
replies
1.9k
views
Merging several DISCOVAR "variant" files
haplotypes phasing variant vcf
updated 24 months ago by 43k • written 9.2 years ago by ★ 2.6k
2
votes
6
replies
4.2k
views
Tophat: # reads mapping to CDS, rRNA, intergenic?
RNA-Seq NGS Tophat
updated 22 months ago by 43k • written 9.1 years ago by ★ 2.6k
0
votes
0
replies
2.6k
views
Comparing RNAseq Samples
NGS RNAseq differential expression
9.1 years ago by Adrian Pelin ★ 2.6k
10
votes
3
replies
18k
views
bwa mem vs bwa aln
SNP bwa illumina vcf
updated 9.1 years ago by ▴ 160 • written 9.7 years ago by ★ 2.6k
4
votes
3
replies
2.0k
views
DiscoSnp++, question about how SNPs called
NGS PopGen DiscoSNP VCF
updated 23 months ago by 43k • written 9.1 years ago by ★ 2.6k
3
votes
1
reply
5.5k
views
Calculating Watterson's Theta and Tajima's Pi from NGS (bam file)
NGS theta pi bam SNP
updated 2.0 years ago by 43k • written 9.2 years ago by ★ 2.6k
2
votes
0
replies
2.2k
views
Importance of the reference genome, it's quality when mapping reads
reference-genome mapping NGS bwa assembly
updated 2.1 years ago by 43k • written 9.3 years ago by ★ 2.6k
1
vote
6
replies
4.9k
views
Pegas import fasta and calculate theta
pegas theta fasta R
updated 2.1 years ago by 43k • written 9.3 years ago by ★ 2.6k
1
vote
1
reply
2.4k
views
Using R to calculate diversity between hundreds of orthologous sequences
R diversity alignment
updated 9.3 years ago by ★ 1.9k • written 9.3 years ago by ★ 2.6k
2
votes
8
replies
2.5k
views
Comparing repetitiveness between 2 assemblies of the same dataset
NGS illumina Assembly heterozygosity
updated 2.1 years ago by 43k • written 9.3 years ago by ★ 2.6k
10
votes
10
replies
10.0k
views
MrBayes: Implementing the LG model
mrbayes prottest substitution
updated 9.4 years ago by 54k • written 10.1 years ago by ★ 2.6k
6
votes
8
replies
5.1k
views
SNP enrichment, how to test for it?
SNPs GO enrichment KOG
updated 2.2 years ago by 43k • written 9.4 years ago by ★ 2.6k
1
vote
3
replies
1.7k
views
Recombination events from single end reads.
recombinant SNPs vcf
updated 2.2 years ago by 43k • written 9.5 years ago by ★ 2.6k
4
votes
7
replies
6.3k
views
Extracting paired-end reads on different contigs from bam file
recombination bam
updated 2.3 years ago by 43k • written 9.5 years ago by ★ 2.6k
7
votes
8
replies
4.4k
views
Mate Pairs Contaminated With Single And Paired End?
tag1 tag2
updated 3.1 years ago by 43k • written 10.2 years ago by ★ 2.6k
1
vote
1
reply
2.6k
views
Recombination detection from command line?
RDP recombination
updated 9.6 years ago by 28k • written 9.6 years ago by ★ 2.6k
11
votes
12
replies
6.4k
views
Selection from population data
popgen watterson pi theta selection
updated 2.3 years ago by 43k • written 9.7 years ago by ★ 2.6k
1
vote
0
replies
2.1k
views
Loss of Heterozygosity from VCF file in non-model organisms
LOH vcf
9.7 years ago by Adrian Pelin ★ 2.6k
1
vote
1
reply
3.1k
views
MLE Approach: Calculate LD (r^2) from unphased data
r2 plink vcf LD
updated 2.3 years ago by 43k • written 9.7 years ago by ★ 2.6k
20
votes
17
replies
13k
views
6 follow
Unexpected outcome: Gene Enrichment using Fisher's Test
KEGG Enrichment R Fishers-Test gene
updated 2.4 years ago by 43k • written 9.7 years ago by ★ 2.6k
0
votes
2
replies
6.3k
views
bwa report multiple alignments
bwa
updated 9.7 years ago by 3.2k • written 9.7 years ago by ★ 2.6k
7
votes
2
replies
8.1k
views
How Does The Samtools Phase Operation Work?
vcf ngs haplotype samtools
updated 2.4 years ago by 43k • written 10.3 years ago by ★ 2.6k
2
votes
9
replies
2.5k
views
Anyone know of Tetraploid NGS available?
k-mer ngs tetraploid
updated 2.4 years ago by 43k • written 9.7 years ago by ★ 2.6k
0
votes
7
replies
3.4k
views
cummeRbund error in loading cuffdiff gene file
cufflinks cummeRbund R
updated 2.4 years ago by 43k • written 9.7 years ago by ★ 2.6k
2
votes
5
replies
2.8k
views
GTF files for cufflinks
cufflinks gtf annotation jgi
updated 2.4 years ago by 43k • written 9.8 years ago by ★ 2.6k
0
votes
0
replies
2.1k
views
KOG Enrichment for high Fst values
Fst KOG enrichment population
updated 9.8 years ago by 20 • written 9.9 years ago by ★ 2.6k
0
votes
0
replies
2.0k
views
VCFTools: Calculation of r^2 fails
vcf vcftools r2
updated 13 months ago by 43k • written 9.9 years ago by ★ 2.6k
1
vote
2
replies
4.4k
views
Plotting LD decay in window
r2 R plot LD
updated 2.5 years ago by 43k • written 9.9 years ago by ★ 2.6k
0
votes
2
replies
1.9k
views
LD r^2 in clonal tetraploids
r^2 popgen
9.9 years ago by Adrian Pelin ★ 2.6k
2
votes
4
replies
4.2k
views
Calculate r^2 from allele frequencies
r2 vcf
updated 2.3 years ago by 43k • written 9.9 years ago by ★ 2.6k
0
votes
0
replies
1.5k
views
Determining abnormalities in synteny blocks
DNA-seq
9.9 years ago by Adrian Pelin ★ 2.6k
0
votes
3
replies
2.0k
views
Test for recombination in a clonal tetraploid?
NGS snp HiSeq
updated 2.6 years ago by 43k • written 9.9 years ago by ★ 2.6k
0
votes
2
replies
2.5k
views
Linkage Disequlibirum (R^2) = recombination?
ngs vcf r2
updated 2.6 years ago by 43k • written 9.9 years ago by ★ 2.6k
1
vote
1
reply
1.7k
views
Building a reference genome for pop differentiation.
DNA-seq NGS pop gen
updated 9.9 years ago by 12k • written 9.9 years ago by ★ 2.6k
0
votes
2
replies
4.0k
views
FST: allele-counts or allele-frequencies?
NGS FST popgen
updated 2.6 years ago by 43k • written 9.9 years ago by ★ 2.6k
0
votes
4
replies
4.5k
views
Merging Bayesian probability values with bootstraps from ML
ML PHYML Bayesian Support
updated 10.0 years ago by 4.9k • written 10.0 years ago by ★ 2.6k
9
votes
8
replies
8.2k
views
bedtools: extracting no coverage regions
bedtools bam coverage
updated 2.6 years ago by 43k • written 10.0 years ago by ★ 2.6k
0
votes
0
replies
2.5k
views
MrBayes, how to judge the quality of a run?
Tracer MrBayes Bayesian
updated 2.6 years ago by 43k • written 10.0 years ago by ★ 2.6k
1
vote
8
replies
6.2k
views
Phylogenetic analysis, combining Bayesian and Maximum Likelihood
mrbayes phylogeny bayesian ML
updated 2.6 years ago by 43k • written 10.0 years ago by ★ 2.6k
1
vote
7
replies
4.2k
views
Best Cnv Software?
ngs paired-end cnv
updated 10.1 years ago by 8.2k • written 10.1 years ago by ★ 2.6k
2
votes
4
replies
3.0k
views
Bwa Map Single And Pe Reads To Ref?
bwa vcf
10.1 years ago by Adrian Pelin ★ 2.6k
0
votes
0
replies
1.8k
views
Detect Recommbination Used Phased Vcf?
vcf variant
10.1 years ago by Adrian Pelin ★ 2.6k
2
votes
7
replies
5.6k
views
Newbler: Merged Miseq Reads + Mate Pairs?
illumina assembly
updated 10.1 years ago by ★ 1.3k • written 10.1 years ago by ★ 2.6k
4
votes
7
replies
4.6k
views
How Do High Fst Compare With Dn/Ds?
fst
updated 10.2 years ago by ▴ 840 • written 10.2 years ago by ★ 2.6k
0
votes
4
replies
2.1k
views
Dating Common Ancestor
ngs vcf
updated 16 months ago by 43k • written 10.2 years ago by ★ 2.6k
0
votes
2
replies
4.1k
views
How To Calculate Recombination Rate From R^2 Data?
ngs recombination
10.2 years ago by Adrian Pelin ★ 2.6k
0
votes
3
replies
6.4k
views
How To Set Tim1 Model In Mrbayes
updated 10.2 years ago by 4.9k • written 10.2 years ago by ★ 2.6k
0
votes
0
replies
2.2k
views
Deltaaic Phyml/Mrbayes
10.2 years ago by Adrian Pelin ★ 2.6k
4
votes
5
replies
2.5k
views
Cnv With Cufflinks?
cnv bwa cufflinks
updated 10.3 years ago by 8.2k • written 10.3 years ago by ★ 2.6k
111 results • Page 2 of 3
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