---
title: "Alignment Data"
date: "`r format(Sys.time(), '%d %B, %Y')`"  
output: 
  html_document:
    theme: readable
    highlight: zenburn
    toc: true
    toc_float: true
    number_sections: true
    code_folding: show
    code_download: true
---


```{r setup, include=FALSE}
library(knitr)
library(tidyverse)
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
)
```
RNA-seq

millipora genome prep

```{r, engine='bash'}
/home/shared/hisat2-2.2.1/hisat2_extract_exons.py \
../data/Amil/ncbi_dataset/data/GCF_013753865.1/genomic.gtf \
> ../output/04-Apulcra-hisat/m_exon.tab
```

```{r, engine='bash'}
head ../output/04-Apulcra-hisat/m_exon.tab

```
```{r, engine='bash'}
/home/shared/hisat2-2.2.1/hisat2_extract_splice_sites.py \
../data/Amil/ncbi_dataset/data/GCF_013753865.1/genomic.gtf \
> ../output/04-Apulcra-hisat/m_splice_sites.tab
```

"${programs_array[hisat2_build]}" \
"${genome_fasta}" \
"${genome_index_name}" \
--exon "${exons}" \
--ss "${splice_sites}" \
-p "${threads}" \
2> hisat2-build_stats.txt



```{r, engine='bash'}
/home/shared/hisat2-2.2.1/hisat2-build \
../data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna \
GCF_013753865.1_Amil_v2.1 \
--exon ../output/04-Apulcra-hisat/m_exon.tab \
--ss ../output/04-Apulcra-hisat/m_splice_sites.tab \
-p 40 \
../data/Amil/ncbi_dataset/data/GCF_013753865.1/genomic.gtf \
2> ../output/04-Apulcra-hisat/hisat2-build_stats.txt
```



# Alignment

Hisat2 alignments
"${programs_array[hisat2]}" \
-x "${genome_index_name}" \
-1 "${fastq_list_R1}" \
-2 "${fastq_list_R2}" \
-S "${sample_name}".sam \
2> "${sample_name}"-hisat2_stats.txt

```{r, engine='bash'}
/home/shared/hisat2-2.2.1/hisat2 \
-x ../output/04-Apulcra-hisat/GCF_013753865.1_Amil_v2.1 \
-p 48 \
-1 ../data/SRR8601366_1.fastq \
-2 ../data/SRR8601366_2.fastq \
-S ../output/04-Apulcra-hisat/SRR8601366_mil.sam \
2>&1 | tee ../output/04-Apulcra-hisat/hisat2_stats.txt
```