---
title: "Diel Expression of Cyanobacteria Genes in the North Pacific Transition Zone"
author: "Kathy Qi"
format: 
  revealjs:
    theme: sky
editor: visual
---

## Research Goals

-   Quantify and visualize cyanobacteria genes related to photoinhibition at diel time scales
-   Hypothesis: *Prochlorococcus* and *Synechococcus* downregulate genes related to photosynthesis and upregulated genes related to oxidative stress during peak irradiance hours.

## Methods

-   Started from trimmed, paired reads of poly-A non-selected Metatranscriptomic samples
-   Used predicted genes from 771 genomes following a [published study](https://zenodo.org/records/12210994)
-   Built an index files using Salmon:

```{bash}
# Build index if it doesn't exist
if [ ! -d "$INDEX_DIR" ]; then
    echo "Building Salmon index..."
    # -k is kmer length, try 31 for now
    salmon index -t "$FASTA" -i "$INDEX_DIR" -k 31 -p $THREADS --keepDuplicates 
else
    echo "Salmon index already exists at $INDEX_DIR"
fi
```

## Methods

-   Aligned transcripts to index file:

```{bash}
# run salmon 
salmon quant -i "$INDEX_DIR" -l A \
-1 "$read1" -2 "$read2" \
-p $THREADS --validateMappings \
-o "$OUTPUT_DIR"
```

## Preliminary Results

-   Resulted in \~1-5% mapping rate for each sample

## Plan for next 4 weeks

-   Analyze the resulting mapped samples and gene counts
-   Identify annotated genes related to photosynthesis and oxidative stres
-   Check for statistical differences between samples at different times of day (dawn vs. noon vs. dusk)
-   If there's time, check for differences in another [published diel study](https://www.nature.com/articles/s41559-021-01606-w) in a different location