---
title: "single sample trim and alignment test"
author: "Megan Ewing"
date: "2024-10-16"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

trimming

```{bash}

# > cutadapt path 'cutadapt'

	    /home/shared/cutadapt-venv/bin/cutadapt \
    	-j 0 \
    	-o ../data/trimmed/M-C-216.trimmed.R1.fastq.gz \
    	-p ../data/trimmed/M-C-216.trimmed.R2.fastq.gz \
    	-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA \
    	-A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT \
    	-q 15,10 \
    	-m 40 \
    	--trim-n \
    	../data/raw/M-C-216_R1_001.fastq.gz \
      ../data/raw/M-C-216_R2_001.fastq.gz \
    	&> ../data/trimmed/cutadapt.log #file path for log file 


```


alignment (hisat)

```{bash}

#index already built

#running hisat
/home/shared/hisat2-2.2.1/hisat2 \
-x ../output/hisat/GCF_026571515.1_index \
-p 48 \
-1 ../data/trimmed/M-C-216.trimmed.R1.fastq.gz \
-2 ../data/trimmed/M-C-216.trimmed.R2.fastq.gz \
-S ../output/hisat/M-C-216.sam \
2>&1 | tee ../output/hisat/hisat2_stats.txt



```


