---
title: "FastQC_pre-trim"
output: html_document
---

Rmd to run FastQC on pre-trimmed RNAseq data from _Pycnopodia helianthoides_ coelomocytes sampled summer/fall 2021 at USGS Marrowstone Field Station as part of the large SSWD _Pycnopodia_ Epidemiology project.      
Personel: Drew Harvell, Alyssa Gehman, TNC, Hakai, USGS, WDFW, UWSAFS. 

All RAW fastq files (Libraries: n = 32) are found on owl: http://owl.fish.washington.edu/nightingales/P_helianthoides/ 

All samples from this project have the beginning of "PSC_" filename. 
Files were later transferred to RAVEN, see below. 

FastQC on Raven lives: `/home/shared/FastQC/fastqc`

```{bash}
/home/shared/FastQC/fastqc -h
```

Check working directory:
```{bash}
pwd
```

<<<<<<< HEAD
=======
Files are stored on Raven in: `pycnornaseq`

Run FASTQC on untrimmed RNAseq .fastq.gz files (08/03/2022):
Below modified from Roberts Lab [Code Snippets](https://robertslab.github.io/resources/code_Snippets/)     
```{bash}
# Set CPU threads to use
threads=48

# Populate array with FastQ files
fastq_array=(/home/shared/8TB_HDD_02/graceac9/pycnornaseq/*.fastq.gz)

# Pass array contents to new variable
fastqc_list=$(echo "${fastq_array[*]}")

# Run FastQC
# NOTE: Do NOT quote ${fastqc_list}
/home/shared/FastQC/fastqc \
--threads ${threads} \
--outdir /home/shared/8TB_HDD_02/graceac9/analyses/pycno/ \
${fastqc_list}
```
>>>>>>> 81fcf3e261236ad841f8aa1d2415a632c3de54ea


 Files are stored on Raven in: `pycnornaseq`

 Run FASTQC on untrimmed RNAseq .fastq.gz files (08/03/2022):
 Below modified from Roberts Lab [Code Snippets](https://robertslab.github.io/resources/code_Snippets/)     
 
```{bash}
 # Set CPU threads to use
 threads=48
 # Populate array with FastQ files
 fastq_array=(/home/shared/8TB_HDD_02/graceac9/pycnornaseq/*.fastq.gz)
 # Pass array contents to new variable
 fastqc_list=$(echo "${fastq_array[*]}")
 # Run FastQC
 # NOTE: Do NOT quote ${fastqc_list}
 /home/shared/FastQC/fastqc \
 --threads ${threads} \
 --outdir /home/shared/8TB_HDD_02/graceac9/analyses/pycno/ \
 ${fastqc_list}
```