multimappings_unique mappings.Rmd

---
title: "multimappings"
output: html_document
date: "2023-10-10"
editor_options: 
  chunk_output_type: console
---

loading data
```{r warning=FALSE, message=FALSE}
hdeg_rep1 <- set_1
udeg_rep1 <- set_1
```

separating multimappings- filtering out with mapq score of 0
```{r warning=FALSE, message=FALSE}
hdeg_rep1_m <- hdeg_rep1 %>% 
  filter(MapQ=="0")
hdeg_rep1_u <- hdeg_rep1 %>% 
  filter(MapQ=="60")
udeg_rep1_m <- udeg_rep1 %>% 
  filter(MapQ=="0")
udeg_rep1_u <- udeg_rep1 %>% 
  filter(MapQ=="60")
```

Distribution plot of read lengths of multimappings
```{r warning=FALSE, message=FALSE}
ggplot(udeg_rep1_m, aes(x=ReadLen)) + geom_histogram(binwidth = 1, col="blue") + ggtitle("Non-degraded- Read lengths of Multi-mappers") + theme_bw() + labs(x="Read Length", y="Number of Reads") + theme(axis.text=element_text(size=16), axis.title=element_text(size=18)) + theme(plot.title = element_text(size=18, face = "bold")) + xlim(0,4000) + ylim(0,500)

ggplot(udeg_rep1_u, aes(x=ReadLen)) + geom_histogram(binwidth = 1, col="blue") + ggtitle("Non-degraded- Read lengths of Unique mappings") + theme_bw() + labs(x="Read Length", y="Number of Reads") + theme(axis.text=element_text(size=16), axis.title=element_text(size=18)) + theme(plot.title = element_text(size=18, face = "bold"))+ xlim(0,4000) + ylim(0,500)

ggplot(hdeg_rep1_m, aes(x=ReadLen)) + geom_histogram(binwidth = 1, col="blue") + ggtitle("Heavily degraded- Read lengths of Multi-mappers") + theme_bw() + labs(x="Read Length", y="Number of Reads") + theme(axis.text=element_text(size=16), axis.title=element_text(size=18)) + theme(plot.title = element_text(size=18, face = "bold"))+ xlim(0,4000)

ggplot(hdeg_rep1_u, aes(x=ReadLen)) + geom_histogram(binwidth = 1, col="blue") + ggtitle("Heavily degraded- Read lengths of Unique Mappings") + theme_bw() + labs(x="Read Length", y="Number of Reads") + theme(axis.text=element_text(size=16), axis.title=element_text(size=18)) + theme(plot.title = element_text(size=18, face = "bold"))+ xlim(0,4000) + ylim(0,230)
```