ligation_ddradseq.Rmd

---
title: "Ligation on `r Sys.Date()`"
output: html_notebook
params:
  num_samples: 240
---
```{r echo=FALSE, message=FALSE}
source("../genomics/scripts/lab_helpers.R")
library(tidyverse)
library(knitr)
library(kableExtra)

print(params)
```



1.  Make a master mix
```{r mix, echo=FALSE}
mix <- readr::read_csv("ingredient, vol
P2_adapter, NA
uL_10x_buffer, NA
uL_ligase, NA
total, NA
") %>% 
  # multiply number of samples by 1.1 for pipetting error
  mutate(
    vol = ifelse(ingredient == "P2_adapter", 2 * ceiling(params$num_samples * 1.1), vol),
    vol = ifelse(ingredient == "uL_10x_buffer", 3 * ceiling(params$num_samples * 1.1), vol),
    vol = ifelse(ingredient == "uL_ligase", 0.8 * (params$num_samples * 1.1), vol), 
    vol = ifelse(ingredient == "total", sum(as.numeric(vol[1:3])), vol)
    )
 
kable(mix) %>%
  kable_styling(latex_options = c("striped"), font_size = 14) %>%
  add_header_above(c("Ligation Master Mix" = 2))
```
2. Add 2uL P1 adapter to each well.  

3. Add 5.8 uL master mix to plates, spin down, and allow reaction to occur at room temperature for 1.5 hours.  

4. Heat kill using the thermocycler.