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BernardoGG / SARS-CoV-2_Genomic_lineages_Ecuador

Identification and analysis of the early transmission dynamics, importations and local circulation of SARS-CoV-2 in Ecuador inferred from genomic data.
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where to find these files? #3

Closed BEAST-Community closed 7 months ago

BEAST-Community commented 3 years ago

meta1 <- read.csv("Data/genetic_data/GISAID_complete_highcoverage_20210107/gisaid_hcov-19_2021_01_0715(1).tsv", sep = "\t", strip.white = TRUE) meta2 <- read.csv("Data/genetic_data/GISAID_complete_highcoverage_20210107/gisaid_hcov-19_2021_01_0715(2).tsv", sep = "\t", strip.white = TRUE) meta3 <- read.csv("Data/genetic_data/GISAID_complete_highcoverage_20210107/gisaid_hcov-19_2021_01_0715(3).tsv", sep = "\t", strip.white = TRUE) meta4 <- read.csv("Data/genetic_data/GISAID_complete_highcoverage_20210107/gisaid_hcov-19_2021_01_0716(4).tsv", sep = "\t", strip.white = TRUE) meta5 <- read.csv("Data/genetic_data/GISAID_complete_highcoverage_20210107/gisaid_hcov-19_2021_01_0716(5).tsv", sep = "\t", strip.white = TRUE) meta6 <- read.csv("Data/genetic_data/GISAID_complete_highcoverage_20210107/gisaid_hcov-19_2021_01_0716(6).tsv", sep = "\t", strip.white = TRUE) meta7 <- read.csv("Data/genetic_data/GISAID_complete_highcoverage_20210107/gisaid_hcov-19_2021_01_0716(7).tsv", sep = "\t", strip.white = TRUE) meta8 <- read.csv("Data/genetic_data/GISAID_complete_highcoverage_20210107/gisaid_hcov-19_2021_01_0716(8).tsv", sep = "\t", strip.white = TRUE) meta9 <- read.csv("Data/genetic_data/GISAID_complete_highcoverage_20210107/gisaid_hcov-19_2021_01_0716(9).tsv", sep = "\t", strip.white = TRUE) meta10 <- read.csv("Data/genetic_data/GISAID_complete_highcoverage_20210107/gisaid_hcov-19_2021_01_0716(10).tsv", sep = "\t", strip.white = TRUE) meta11 <- read.csv("Data/genetic_data/GISAID_complete_highcoverage_20210107/gisaid_hcov-19_2021_01_0716(11).tsv", sep = "\t", strip.white = TRUE) meta12 <- read.csv("Data/genetic_data/GISAID_complete_highcoverage_20210107/gisaid_hcov-19_2021_01_0716(12).tsv", sep = "\t", strip.white = TRUE) meta13 <- read.csv("Data/genetic_data/GISAID_complete_highcoverage_20210107/gisaid_hcov-19_2021_01_0716(13).tsv", sep = "\t", strip.white = TRUE) meta14 <- read.csv("Data/genetic_data/GISAID_complete_highcoverage_20210107/gisaid_hcov-19_2021_01_0716(14).tsv", sep = "\t", strip.white = TRUE) meta15 <- read.csv("Data/genetic_data/GISAID_complete_highcoverage_20210107/gisaid_hcov-19_2021_01_0716(15).tsv", sep = "\t", strip.white = TRUE) meta16 <- read.csv("Data/genetic_data/GISAID_complete_highcoverage_20210107/gisaid_hcov-19_2021_01_0716(16).tsv", sep = "\t", strip.white = TRUE) meta17 <- read.csv("Data/genetic_data/GISAID_complete_highcoverage_20210107/gisaid_hcov-19_2021_01_0716(17).tsv", sep = "\t", strip.white = TRUE) meta18 <- read.csv("Data/genetic_data/GISAID_complete_highcoverage_20210107/gisaid_hcov-19_2021_01_0716(18).tsv", sep = "\t", strip.white = TRUE) meta19 <- read.csv("Data/genetic_data/GISAID_complete_highcoverage_20210107/gisaid_hcov-19_2021_01_0716(19).tsv", sep = "\t", strip.white = TRUE) meta20 <- read.csv("Data/genetic_data/GISAID_complete_highcoverage_20210107/gisaid_hcov-19_2021_01_0716(20).tsv", sep = "\t", strip.white = TRUE) meta21 <- read.csv("Data/genetic_data/GISAID_complete_highcoverage_20210107/gisaid_hcov-19_2021_01_0716(21).tsv", sep = "\t", strip.white = TRUE) meta22 <- read.csv("Data/genetic_data/GISAID_complete_highcoverage_20210107/gisaid_hcov-19_2021_01_0716(22).tsv", sep = "\t", strip.white = TRUE) meta23 <- read.csv("Data/genetic_data/GISAID_complete_highcoverage_20210107/gisaid_hcov-19_2021_01_0716(23).tsv", sep = "\t", strip.white = TRUE)

BernardoGG commented 3 years ago

These were downloaded directly from GISAID when the FASTA files were downloaded. I've added two files as examples in the metadata directory, mostly as a reference of the file structure. It should be noted that in that same directory there is a file named GISAID_hCoV-19_20210107_EC_all.tsv, this file contains the information produced by the referenced code. The reason why it was originally imported into the R working environment as separate files is that GISAID only allowed for a limited number of sequences to be downloaded at any one time.

BEAST-Community commented 3 years ago

thanks, i like your research very much. Thanks for your help.