-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathpartial-udg-double-stranded.qmd
43 lines (30 loc) · 2.13 KB
/
partial-udg-double-stranded.qmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
# Partial UDG (double-stranded)
<!-- {#fig-double-stranded-caricature} -->
_CARICATURE PLOT GOES HERE_
```{r}
#| label: fig-udg-double-stranded
#| fig-cap: Example of a smiley plot of a double-stranded 'partial UDG' or 'UDG half' library. Data taken from library VLI092.A0101 (ERR8958796) of [@Andrades_Valtuena2022-tq]. Damage data generated using [DamageProfiler](/intro.qmd) and plotted using R and tidyverse packages [@Wickham2019-ot].
#| echo: false
#| warning: false
#| error: false
library(glossary)
glossary::glossary_path("glossary.yml")
glossary::glossary_popup("hover")
library(readr)
library(tidyr)
library(dplyr)
library(ggplot2)
library(patchwork)
source("assets/src/R/style.r")
source("assets/src/R/damage-profiler.r")
type_colours <- type_colours_dp
raw_5p <- readr::read_tsv("assets/data/partial-udg-double-stranded/5p_freq_misincorporations.txt", comment = "#")
raw_3p <- readr::read_tsv("assets/data/partial-udg-double-stranded/3p_freq_misincorporations.txt", comment = "#")
long_5p <- pivot_longer_freqmisincorporat(raw_5p, reverse = FALSE, type_colours = type_colours)
long_3p <- pivot_longer_freqmisincorporat(raw_3p, reverse = TRUE, type_colours = type_colours)
smiley_5p <- plot_longer_freqmisincorporat(long_5p, reverse = FALSE, type_colours)
smiley_3p <- plot_longer_freqmisincorporat(long_3p, reverse = TRUE, type_colours)
smiley_5p + smiley_3p
```
The smiley plot presented here has been generated from a double-stranded 'partial UDG' or 'UDG-half' library. `r glossary('UDG')` or USER Treatment consists of enzymatically cleaving off ends of molecules when a uracil is present. Whereas complete-UDG UDG full runs the protocol long enough for all DNA molecules to be enzymatically modified, partial UDG stops early, meaning that a small number of reads retain uracils on the last base. This allows for simultaneous authentication of damage, but makes it easier to then _in silico_ remove damage by 'trimming' off one base from either end of each read, so you can ensure you do not incorporate damaged bases into downstream analyses.
<!-- TODO complete dDescription -->