---
title: "14-kallisto"
author: "Steven Roberts"
date: "`r format(Sys.time(), '%d %B, %Y')`"  
output: 
  github_document:
    toc: true
    toc_depth: 3
    number_sections: true
    html_preview: true
  html_document:
    theme: readable
    highlight: zenburn
    toc: true
    toc_float: true
    number_sections: true
    code_folding: show
    code_download: true
editor_options: 
  markdown: 
    wrap: sentence
---

```{r setup, include=FALSE}
library(knitr)
library(tidyverse)
library(kableExtra)
library(DT)
library(Biostrings)
library(tm)
library(pheatmap)
library(DESeq2)
knitr::opts_chunk$set(
  echo = TRUE,         # Display code chunks
  eval = FALSE,         # Evaluate code chunks
  warning = FALSE,     # Hide warnings
  message = FALSE,     # Hide messages
  fig.width = 6,       # Set plot width in inches
  fig.height = 4,      # Set plot height in inches
  fig.align = "center", # Align plots to the center
  comment = ""         # Prevents appending '##' to beginning of lines in code output
)
```

# Differentially Expressed Genes
 


# Reads

```{r, engine='bash', eval=TRUE}
ls /home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/data/raw-trimmed/
```


# Genome


```{r, engine='bash'}
cd ../data

/home/shared/datasets download genome accession GCF_036588685.1 --include gff3,gtf,rna,cds,protein,genome,seq-report
```

```{bash}
cd ../data 
unzip ncbi_dataset.zip
```

```{r, engine='bash', eval=TRUE}
ls ../data/ncbi_dataset/data/GCF_036588685.1

```




```{bash}
/home/shared/kallisto/kallisto index \
-i ../output/14-kallisto-ng/cds.index \
../data/ncbi_dataset/data/GCF_036588685.1/cds_from_genomic.fna
```


```{bash}
find /home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/data/raw-trimmed/*_L099_R1_cmb.trim.fastq.gz | xargs basename -s _L099_R1_cmb.trim.fastq.gz \
| xargs -I{} sh -c '/home/shared/kallisto/kallisto quant \
-i ../output/14-kallisto-ng/cds.index \
-o ../output/kallisto_01/{} \
-t 20 \
--fr-stranded ../data/{}_R1.fastq.gz \
/home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/data/raw-trimmed/{}_L099_R1_cmb.trim.fastq.gz
> ../output/kallisto_01/{}_kallisto.out
```








```{r, engine='bash'}
eval "$(/opt/anaconda/anaconda3/bin/conda shell.bash hook)"
conda activate
which multiqc


multiqc ../output/13-Hisat/ \
-o ../output/13-Hisat/
```