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Bioinformatics Pipeline for MalariaGen's Pf3k and MalariaGen Community (PNG) WGS analysis which is used to characterise diversity analysis of vaccine candidate antigens

Shell 68.90% Python 7.64% R 23.46%

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naung-et-al-2021's Issues

Questions on Fig. 1

Hi @myonaung , Regarding the ridgeline plot in Fig. 1, my understanding is that you used the Tajima's D values for each of the windows for each of the antigens. Am I correct?

Example files for reproducing the R code.

Hi @myonaung,

Thank you for sharing the code.

In the two lines below, we do not see the corresponding files provided in the github link:

Naung-et-al-2021/Phasing_Haplotype/pf3k_antigen.Rmd

Line 68 in 89143c5

func_annotations <- readr::read_rds("pf3kv5_functional_annotations_filtered.rds")

Naung-et-al-2021/Phasing_Haplotype/pf3k_antigen.Rmd

Line 349 in 89143c5

cds_seq <- read.dna(paste0("ref", gene, ".1.fasta"), format="fasta") %>% as.character %>% as.vector %>% toupper

Could you please let us know what columns are included in pf3kv5_functional_annotations_filtered.rds and what are the *.1.fasta files? Thanks again!

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