---
title: "Week 5 Presentation"
format: revealjs
editor: visual
---

## FISH 546 Week 5 Presentation

Sarah Yerrace

Invasive Lionfish Gut Content Metabarcoding

![Red Lionfish (*Pterois volitans*) (Include image, CHECK)](https://media.istockphoto.com/id/1208022389/photo/common-lionfish.jpg?s=612x612&w=0&k=20&c=L_3RCsBhqKFKFeOkDpuEAW7r-zls-E-CVLVXWPKxskM=)

## One) Clearly Demonstrate Goal

-Start: Raw sequences from COI (mtDNA)

-End: Taxon assignments to sequences

JonahVentures technically does this for me. I want to do it better with different database

## Two) Methods taken

One of many fastQ files

```{r, echo=FALSE, eval=TRUE}
sequence <- read.csv("../Data/JV173_UniCOI_Tornabene_S043447.1.R1.fastq.gz")
head(sequence)
```

(Show parts of initial data, CHECK)

## Two) Methods taken

Here's sneak peak of my metadata file

```{r, echo=FALSE, eval=TRUE}
metadata <- read.csv("../metadata.csv")
head(metadata)
```


## Two) Methods taken

| Sample Name | Locus | Well | Set | File 1
|------|------|------| ------|  ------|
| Test 1 | Leray_COI | A1 | 1 | JV173_UniCOI_Tornabene_S043447.1.R1 |
| Test 2 | Leray_COI | B1 | 1 | JV173_UniCOI_Tornabene_S043448.1.R1 |
| Test 3 | Leray_COI | C1 | 1 | JV173_UniCOI_Tornabene_S043449.1.R1 |
| Test 4 | Leray_COI | D1 | 1 | JV173_UniCOI_Tornabene_S043450.1.R1 |
| Test 5 | Leray_COI | C1 | 1 | JV173_UniCOI_Tornabene_S043451.1.R1 |


(table included, CHECK)

## Two) Methods taken

Show core code

```{r, eval=FALSE, echo=TRUE}

## run cutadapt script (see scripts folder) with all the original FASTQ files from Ventures raw sequences to remove the primers at both ends of each sequence

fastqs <- "../Data/"

F1s <- sort(list.files(fastqs, pattern="R1.fastq", full.names = TRUE))
R1s <- sort(list.files(fastqs, pattern="R2.fastq", full.names = TRUE))

sample.names <- str_replace(basename(F1s), "_R1.fastq","")


```

## Three) Preliminary Results

This is using the taxon assingment provided by JonahVentures from just N=4 of N=132 lionfish

```{r, echo=TRUE, eval=TRUE}
#| code-line-numbers: "2"
prelim <- read.csv("../Output/JVB1606-UniCOI-read-data.csv")
hist(x=prelim$X..match, main= "Sequence Percent Match", xlab="% Match")
```

Make a plot from code, CHECK, highlight line of code, CHECK

## Four) Outline Steps for the Future

Meet with Marta next week

Run Blast

Remove Lionfish reads

