CDF export

1. On the GC-MS computer, open Enhanced Data Analysis
2. File > Export Data To .AIA Format, Create New Directory (“OK”) > Desktop (create a folder with a name you will remember)
3. Select all the datafiles you wish to analyze and process them, saving the output into the folder you just created
4. Copy the .D files for the samples you wish to analyze to the same folder
5. Move this folder to your personal computer
6. Create one folder for each sample, and put the corresponding .CDF file into that folder.

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# reads <- readFasta("https://drive.google.com/file/d/1r6E0U5LyYwjWenxy9yqh5QQ2mq1umWOW/view?usp=sharing")

# # post <- readFasta("/Users/bust0037/Desktop/ragtag.scaffold.fasta")
# n_chroms <- 18

# pb <- progress::progress_bar$new(total = n_chroms)

# out <- list()

# for (i in 1:n_chroms) {

#   pb$tick()

#   dat <- strsplit(substr(as.character(post[i]), 1, 50000000), "")[[1]]
  
#   b <- rle(dat)

#   # Create a data frame
#   dt <- data.frame(number = b$values, lengths = b$lengths, scaff = i)
#   # Get the end
#   dt$end <- cumsum(dt$lengths)
#   # Get the start
#   dt$start <- dt$end - dt$lengths + 1

#   # Select columns
#   dt <- dt[, c("number", "start", "end", "scaff")]
#   # Sort rows
#   dt <- dt[order(dt$number), ]

#   dt %>%
#     filter(number == "N") -> N_dat

#   out[[i]] <- N_dat

# }

# out <- do.call(rbind, out)


# chroms <- data.frame(
#   lengths = post@ranges@width[1:n_chroms],
#   scaff = seq(1,n_chroms,1)
# )

# ggplot() +
#   statebins:::geom_rrect(data = chroms, aes(xmin = 0, xmax = lengths, ymin = -1, ymax = 1, fill = scaff), color = "black") +
#   geom_rect(data = out, aes(xmin = start, xmax = end, ymin = -0.95, ymax = 0.95), color = "white", fill = "white", size = 0.08) +
#   facet_grid(scaff~.) +
#   scale_fill_viridis(end = 0.8) +
#   theme_classic()

# ggplot() +
#   geom_rect(data = filter(chroms, scaff == 1 | scaff == 2), aes(xmin = 0, xmax = lengths, ymin = -1, ymax = 1, fill = scaff), color = "black") +
#   geom_rect(data = filter(out, scaff == 1 | scaff == 2), aes(xmin = start, xmax = end, ymin = -0.95, ymax = 0.95), color = "white", fill = "white", size = 0.08) +
#   facet_grid(scaff~.) +
#   scale_y_continuous(limits = c(-2,2)) +
#   scale_fill_viridis(end = 0.8) +
#   theme_classic() +
#   coord_polar()

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