---
title: "Long non-coding RNA discovery in _Pocillopora verrucosa_"
format: revealjs
editor: visual
---

## Project Background and Goal

-   Long non-coding RNAs (lncRNAs) are a type of RNA molecule that are longer than 200 nucleotides and do not encode for proteins.

-   Play important roles in various cellular processes

    -   gene expression regulation

    -   chromatin remodeling

    -   post-transcriptional processing

## Project Background and Goals

-   RNA-seq data from corals

    -   Treatment: nutrient exposure

-   Identify long non-coding RNAs (lncRNAs) in RNA-seq data

    -   Develop a list of all lncRNAs found in each sample for use in differential and/or correlation expression analysis

## RNA-seq Data

-   Trimmed fastq files

```{bash}
head /home/shared/8TB_HDD_02/zbengt/github/zach-lncRNA/data/C17_R1_001.fastq
```

## Methods: Workflow

![](workflow.png)

## Highlight: HISAT2

-   Run HISAT2 over all files to align

```{r, eval=FALSE, echo=TRUE}
#| code-line-numbers: "1|2"
find /home/shared/8TB_HDD_01/pver/*gz \
| xargs basename -s _R1_001.fastq.gz | xargs -I{} \
/home/shared/hisat2-2.2.1/hisat2 \
-x ../output/Pver_genome_assembly_v1.0-valid.index \
-p 8 \
-1 /home/shared/8TB_HDD_01/pver/{}_R1_001.fastq.gz \
-2 /home/shared/8TB_HDD_01/pver/{}_R2_001.fastq.gz \
-S /home/shared/8TB_HDD_01/pver/hisat-output/{}-valid.sam
```

## Highlight: CPC2

```{r, eval=FALSE, echo=TRUE}
eval "$(/opt/anaconda/anaconda3/bin/conda shell.bash hook)"

python /home/shared/CPC2_standalone-1.0.1/bin/CPC2.py 
-i /home/shared/8TB_HDD_01/pver/bedtools-output/merged_lncRNA_candidates.fasta 
-o /home/shared/8TB_HDD_01/pver/cpc2-output/cpc2_results.txt
```

## Current Place

```{r, eval=FALSE, echo=TRUE}
#| code-line-numbers: "6"
awk 'NR>1 && $9 < 0 {print $1}' /home/shared/8TB_HDD_01/pver/cpc2-output
/cpc2_results.txt.txt > /home/shared/8TB_HDD_01/pver/cpc2-output
/noncoding_transcripts_ids.txt
grep -Fwf /home/shared/8TB_HDD_01/pver/cpc2-output/noncoding_transcripts_ids.txt 
/home/shared/8TB_HDD_01/pver/bedtools-output/merged_lncRNA_candidates.fasta > ~ 
  /github/zach-lncRNA/output/merged_final_lncRNAs.gtf
```

-   List of lncRNA transcript IDs for all samples

```{bash}
head ~/github/zach-lncRNA/output/merged_final_lncRNAs.gtf
```

## Where I'm headed...

| Week 6     | Kallisto count matrices                 |
|------------|-----------------------------------------|
| Week 7-8   | Co-expression with coding RNAs          |
| Weeks 9-10 | DESEq2, lncRNA sensitivity to treatment |
