Homa Papoli Yazdi

Hello, I have a question about calculating confidence interval for the PSMC method. I have done the bootstrapping step. To calculate the confidence interval, I am using the maximum error...

Confidence intervals

4

Hi, I was wondering how are the confidence intervals calculated for pairwise LD calculation using r^2? My LD calculation corresponds very well with patterns of genetic diversity and recombination rate,...

Hi, Thanks a lot for the great tutorial. The game works perfectly on my computer when I open two clients but when I try it in two different computers, the...

Tracer plots for LDhat run

1

Hello, I ran _interval_ on 2000 SNPs of a region about 300 Kb. I have 10 diploid individuals. I ran interval with block penalty of 5, 10 million iterations and...

interval for sex chromosomes

2

Hello, I was wondering how I could use the `interval` program of LDhat to generate sex-averaged rho for sex chromosomes where females are diploid and males are haploid? Having 5...

Composite-likelihood and rho plot

3

Hello, Thank you for your software. I was wondering what does it mean when the composite likelihood plateaus for different values of rho as shown in the figure:  Thank...

Fastp does not remove G homopolymers

1

Hello, In my Illumina NovaSeq read, I have many G and C homopolymer reads. I used fastp --trim_poly_g option. However, this option detects reads with at least 10 Gs at...

Tetraploid species

5

Hello, Thank you so much for the great software and the time you put in helping us with our questions. I have troubles understanding my smudgeplot. I have used following...

Hexaploid interpretation and genome size inconsistency

1

Hello, I am sorry for posting this here as this is more a genomescope issue than smudgeplot. We know these samples are hexaploid from flow cytometry. I have two questions:...