---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
layout: post
title: FastQ QC and Trimming - E5 Coral RNA-seq Data for A.pulchra P.evermanni and P.meandrina Using FastQC fastp and MultiQC on Mox
date: '2023-05-19 10:49'
tags: 
  - mox
  - FastQC
  - fastp
  - MultiQC
  - E5
  - coral
  - Acropora pulchra
  - Porites evermanni
  - Pocillopora meandrina
categories: 
  - 2023
  - E5
---
After [downloading](https://robertslab.github.io/sams-notebook/posts/2023/2023-05-16-Data-Received-Coral-RNA-seq-Data-from-Azenta-Project-30-789513166/) and then [reorganizing the E5 coral RNA-seq data from Azenta project 30-789513166](https://robertslab.github.io/sams-notebook/2023/05/17/Data-Management-E5-Coral-RNA-seq-and-sRNA-seq-Reorganizing-and-Renaming/), I ran FastQC for initial quality checks, followed by trimming with `fastp`, and then final QC with FastQC/MultiQC. This was performed on all three species in the data sets: _A.pulchra_, _P.evermanni_, and _P.meandrina_. All aspects were run on Mox.

Skip to [RESULTS](#results).

SLURM Script (GitHub):

- [20230519-E5_coral-fastqc-fastp-multiqc-RNAseq.sh](https://github.com/RobertsLab/sams-notebook/blob/master/sbatch_scripts/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq.sh)

```bash
#!/bin/bash
## Job Name
#SBATCH --job-name=20230519-E5_coral-fastqc-fastp-multiqc-RNAseq
## Allocation Definition
#SBATCH --account=srlab
#SBATCH --partition=srlab
## Resources
## Nodes
#SBATCH --nodes=1
## Walltime (days-hours:minutes:seconds format)
#SBATCH --time=2-00:00:00
## Memory per node
#SBATCH --mem=120G
##turn on e-mail notification
#SBATCH --mail-type=ALL
#SBATCH --mail-user=samwhite@uw.edu
## Specify the working directory for this job
#SBATCH --chdir=/gscratch/scrubbed/samwhite/outputs/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq

### FastQC and fastp trimming of E5 coral species RNA-seq data from 202230515.



### fastp expects input FastQ files to be in format: RNA-ACR-178-S1-TP2_R1_001.fastq.gz


###################################################################################
# These variables need to be set by user

## Assign Variables

# Set FastQ filename patterns
fastq_pattern='*.fastq.gz'
R1_fastq_pattern='*_R1_*.fastq.gz'
R2_fastq_pattern='*_R2_*.fastq.gz'

# Set number of CPUs to use
threads=40

# Input/output files
trimmed_checksums=trimmed_fastq_checksums.md5
fastq_checksums=input_fastq_checksums.md5


# Data directories
reads_dir=/gscratch/srlab/sam/data

# Species array (must match directory name usage)
species_array=("A_pulchra" "P_evermanni" "P_meandrina")

## Inititalize arrays
raw_fastqs_array=()
R1_names_array=()
R2_names_array=()

# Paths to programs
fastp=/gscratch/srlab/programs/fastp.0.23.1
fastqc=/gscratch/srlab/programs/fastqc_v0.11.9/fastqc
multiqc=/gscratch/srlab/programs/anaconda3/bin/multiqc

# Programs associative array
declare -A programs_array
programs_array=(
[fastqc]="${fastqc}"
[fastp]="${fastp}" \
[multiqc]="${multiqc}"
)


###################################################################################

# Exit script if any command fails
set -e

# Load Python Mox module for Python module availability
module load intel-python3_2017

# Capture date
timestamp=$(date +%Y%m%d)


# Set working directory
working_dir=$(pwd)

for species in "${species_array[@]}"
do

    ## Inititalize arrays
    raw_fastqs_array=()
    R1_names_array=()
    R2_names_array=()
    fastq_array_R1=()
    fastq_array_R2=()
    trimmed_fastq_array=()


    echo "Creating ${species} directory and subdirectories..." 

    mkdir --parents "${species}/raw_fastqc" "${species}/trimmed"

    # Change to raw_fastq directory
    cd "${species}/raw_fastqc"


    # FastQC output directory
    output_dir=$(pwd)

    echo "Now in ${PWD}."

    # Sync raw FastQ files to working directory
    echo ""
    echo "Transferring files via rsync..."

    rsync --archive --verbose \
    ${reads_dir}/${species}/RNAseq/${fastq_pattern} .

    echo ""
    echo "File transfer complete."
    echo ""

    ### Run FastQC ###

    ### NOTE: Do NOT quote raw_fastqc_list
    # Create array of trimmed FastQs
    raw_fastqs_array=(${fastq_pattern})

    # Pass array contents to new variable as space-delimited list
    raw_fastqc_list=$(echo "${raw_fastqs_array[*]}")

    echo "Beginning FastQC on raw reads..."
    echo ""

    # Run FastQC
    ${programs_array[fastqc]} \
    --threads ${threads} \
    --outdir ${output_dir} \
    ${raw_fastqc_list}

    echo "FastQC on raw reads complete!"
    echo ""

    ### END FASTQC ###

    ### RUN MULTIQC ###
    echo "Beginning MultiQC on raw FastQC..."
    echo ""

    ${multiqc} .

    echo ""
    echo "MultiQC on raw FastQ complete."
    echo ""

    ### END MULTIQC ###

    # Create arrays of fastq R1 files and sample names
    # Do NOT quote R1_fastq_pattern variable
    for fastq in ${R1_fastq_pattern}
    do
    fastq_array_R1+=("${fastq}")

    # Use parameter substitution to remove all text up to and including last "." from
    # right side of string.
    R1_names_array+=("${fastq%%.*}")
    done

    # Create array of fastq R2 files
    # Do NOT quote R2_fastq_pattern variable
    for fastq in ${R2_fastq_pattern}
    do
    fastq_array_R2+=("${fastq}")

    # Use parameter substitution to remove all text up to and including last "." from
    # right side of string.
    R2_names_array+=("${fastq%%.*}")
    done


    # Create MD5 checksums for raw FastQs
    for fastq in ${fastq_pattern}
    do
        echo "Generating checksum for ${fastq}"
        md5sum "${fastq}" | tee --append ${fastq_checksums}
        echo ""
    done


    ### RUN FASTP ###

    # Run fastp on files
    # Adds JSON report output for downstream usage by MultiQC
    # Trims 20bp from 5' end of all reads
    # Trims 20bp from 3' end of all reads
    # Trims poly G, if present
    # Uses parameter substitution (e.g. ${R1_sample_name%%_*})to rm the _R[12] for report names.
    echo "Beginning fastp trimming."
    echo ""

    for index in "${!fastq_array_R1[@]}"
    do
        R1_sample_name="${R1_names_array[index]}"
        R2_sample_name="${R2_names_array[index]}"
        ${fastp} \
        --in1 ${fastq_array_R1[index]} \
        --in2 ${fastq_array_R2[index]} \
        --detect_adapter_for_pe \
        --trim_poly_g \
        --trim_front1 20 \
        --trim_front2 20 \
        --thread ${threads} \
        --html "../trimmed/${R1_sample_name%%_*}".fastp-trim."${timestamp}".report.html \
        --json "../trimmed/${R1_sample_name%%_*}".fastp-trim."${timestamp}".report.json \
        --out1 "../trimmed/${R1_sample_name}".fastp-trim."${timestamp}".fastq.gz \
        --out2 "../trimmed/${R2_sample_name}".fastp-trim."${timestamp}".fastq.gz
        
        # Move to trimmed directory
        # This is done so checksums file doesn't include excess path in
        cd ../trimmed

        echo "Moving to ${PWD}."
        echo ""

        # Generate md5 checksums for newly trimmed files
        {
            md5sum "${R1_sample_name}".fastp-trim."${timestamp}".fastq.gz
            md5sum "${R2_sample_name}".fastp-trim."${timestamp}".fastq.gz
        } >> "${trimmed_checksums}"


        # Go back to raw reads directory
        cd ../raw_fastqc

        echo "Moving to ${PWD}"
        echo ""
        
        # Remove original FastQ files
        echo ""
        echo " Removing ${fastq_array_R1[index]} and ${fastq_array_R2[index]}."
        
        rm "${fastq_array_R1[index]}" "${fastq_array_R2[index]}"
    done

    echo ""
    echo "fastp trimming complete."
    echo ""

    ### END FASTP ###


    ### RUN FASTQC ON TRIMMED READS ###

    ### NOTE: Do NOT quote ${trimmed_fastqc_list}

    # Moved to trimmed reads directory
    cd ../trimmed

    echo "Moving to ${PWD}"
    echo ""

    # FastQC output directory
    output_dir=$(pwd)

    # Create array of trimmed FastQs
    trimmed_fastq_array=(*fastp-trim*.fastq.gz)

    # Pass array contents to new variable as space-delimited list
    trimmed_fastqc_list=$(echo "${trimmed_fastq_array[*]}")

    # Run FastQC
    echo "Beginning FastQC on trimmed reads..."
    echo ""
    ${programs_array[fastqc]} \
    --threads ${threads} \
    --outdir ${output_dir} \
    ${trimmed_fastqc_list}

    echo ""
    echo "FastQC on trimmed reads complete!"
    echo ""

    ### END FASTQC ###

    ### RUN MULTIQC ###
    echo "Beginning MultiQC on trimmed reads data..."
    echo ""

    ${multiqc} .

    echo ""
    echo "MultiQC on trimmed reads data complete."
    echo ""

    ### END MULTIQC ###

    cd "${working_dir}"

done

####################################################################

# Capture program options
if [[ "${#programs_array[@]}" -gt 0 ]]; then
  echo "Logging program options..."
  for program in "${!programs_array[@]}"
  do
    {
    echo "Program options for ${program}: "
    echo ""
    # Handle samtools help menus
    if [[ "${program}" == "samtools_index" ]] \
    || [[ "${program}" == "samtools_sort" ]] \
    || [[ "${program}" == "samtools_view" ]]
    then
      ${programs_array[$program]}

    # Handle DIAMOND BLAST menu
    elif [[ "${program}" == "diamond" ]]; then
      ${programs_array[$program]} help

    # Handle NCBI BLASTx menu
    elif [[ "${program}" == "blastx" ]]; then
      ${programs_array[$program]} -help
    fi
    ${programs_array[$program]} -h
    echo ""
    echo ""
    echo "----------------------------------------------"
    echo ""
    echo ""
  } &>> program_options.log || true

    # If MultiQC is in programs_array, copy the config file to this directory.
    if [[ "${program}" == "multiqc" ]]; then
      cp --preserve ~/.multiqc_config.yaml multiqc_config.yaml
    fi
  done
fi


# Document programs in PATH (primarily for program version ID)
{
date
echo ""
echo "System PATH for $SLURM_JOB_ID"
echo ""
printf "%0.s-" {1..10}
echo "${PATH}" | tr : \\n
} >> system_path.log
```
---

Took approximately 2hrs to run:

![Runtime for Mox job showing 2hrs, 3mins, and 39secs.](https://github.com/RobertsLab/sams-notebook/blob/master/images/screencaps/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq.png?raw=true)

# RESULTS

Output folders:

### _A.pulchra_

    #### Raw FastQs:

  - MultiQC Report (HTML)

    - [A_pulchra/raw_fastqc/multiqc_report.html](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/A_pulchra/raw_fastqc/multiqc_report.html)

  - MD5 checksums (text)

    - [A_pulchra/raw_fastqc/input_fastq_checksums.md5](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/A_pulchra/raw_fastqc/input_fastq_checksums.md5)

    #### Trimmed FastQs:

  - MultiQC Report (HTML)

    - [A_pulchra/trimmed/multiqc_report.html](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/A_pulchra/trimmed/multiqc_report.html)

  - FastQ (gzipped)

    - [RNA-ACR-140-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/A_pulchra/trimmed/RNA-ACR-140-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz) (2.9G)

      - MD5: `eef049ee0098417d77990b6dd6a0579e`

    - [RNA-ACR-140-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/A_pulchra/trimmed/RNA-ACR-140-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz) (3.0G)

      - MD5: `e0afac6164512ef22e695f7bfd14329e`

    - [RNA-ACR-145-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/A_pulchra/trimmed/RNA-ACR-145-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz) (2.6G)

      - MD5: `89fd1fbcd090132ee4be4523615c62e7`

    - [RNA-ACR-145-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/A_pulchra/trimmed/RNA-ACR-145-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz) (2.6G)

      - MD5: `1344e89bcb77ec9b2a62a74062410bcc`

    - [RNA-ACR-150-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/A_pulchra/trimmed/RNA-ACR-150-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz) (2.6G)

      - MD5: `6f97d5b6bc43afdb10209147d8079674`

    - [RNA-ACR-150-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/A_pulchra/trimmed/RNA-ACR-150-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz) (2.7G)

      - MD5: `7df99937e219fea0780c4e0445e6bebe`

    - [RNA-ACR-173-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/A_pulchra/trimmed/RNA-ACR-173-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz) (2.9G)

      - MD5: `fa620acd4713931ae91c888579ec8d1c`

    - [RNA-ACR-173-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/A_pulchra/trimmed/RNA-ACR-173-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz) (3.0G)

      - MD5: `5ee3263192a30e3e7d294895211d4499`

    - [RNA-ACR-178-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/A_pulchra/trimmed/RNA-ACR-178-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz) (2.6G)

      - MD5: `9b66f6ee9200dc4c05d16273e0fb6eb4`

    - [RNA-ACR-178-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/A_pulchra/trimmed/RNA-ACR-178-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz) (2.7G)

      - MD5: `284c36d72ead05f11cf7a7524ca7c916`

---


### _P.evermanni_

    #### Raw FastQs:

  - MultiQC Report (HTML)

    - [P_evermanni/raw_fastqc/multiqc_report.html](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_evermanni/raw_fastqc/multiqc_report.html)

  - MD5 checksums (text)

    - [P_evermanni/raw_fastqc/input_fastq_checksums.md5](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_evermanni/raw_fastqc/input_fastq_checksums.md5)

    #### Trimmed FastQs:

  - MultiQC Report (HTML)

    - [P_evermanni/trimmed/multiqc_report.html](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_evermanni/trimmed/multiqc_report.html)

  - FastQs (gzipped)

    - [RNA-POR-71-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_evermanni/trimmed/RNA-POR-71-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz) (2.5G)

      - MD5: `a622b00b0553fc35d62896b0b6763331`

    - [RNA-POR-71-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_evermanni/trimmed/RNA-POR-71-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz) (2.6G)

      - MD5: `b5f764aa1727d92a8cf74b0995724df6`

    - [RNA-POR-73-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_evermanni/trimmed/RNA-POR-73-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz) (2.2G)

      - MD5: `3168aeb2cb7790d7c1e6584a992ab5d7`

    - [RNA-POR-73-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_evermanni/trimmed/RNA-POR-73-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz) (2.4G)

      - MD5: `1069960c8446b130f5b3810e1e9870c2`

    - [RNA-POR-76-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_evermanni/trimmed/RNA-POR-76-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz) (2.4G)

      - MD5: `c08c9e6385524793a072d4c14721330e`

    - [RNA-POR-76-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_evermanni/trimmed/RNA-POR-76-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz) (2.5G)

      - MD5: `8ed83046e639f05d1227b74fe87d9bdc`

    - [RNA-POR-79-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_evermanni/trimmed/RNA-POR-79-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz) (2.1G)

      - MD5: `9ecddf149b27f0b18c7505f58d2e9481`

    - [RNA-POR-79-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_evermanni/trimmed/RNA-POR-79-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz) (2.3G)

      - MD5: `55ffc991dffd9c9b2f48e8138e499373`

    - [RNA-POR-82-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_evermanni/trimmed/RNA-POR-82-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz) (2.6G)

      - MD5: `df6f11bb9e44165889a4984d5a160257`

    - [RNA-POR-82-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_evermanni/trimmed/RNA-POR-82-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz) (2.7G)

      - MD5: `b4fbf6e9522ba299e2e8bbd249a9aa0d`

---

### _P.meandrina_

    #### Raw FastQs:

  - MultiQC Report (HTML)

    - [P_meandrina/raw_fastqc/multiqc_report.html](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_meandrina/raw_fastqc/multiqc_report.html)

  - MD5 checksums (text)

    - [P_meandrina/raw_fastqc/input_fastq_checksums.md5](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_meandrina/raw_fastqc/input_fastq_checksums.md5)

    #### Trimmed FastQs:

  - MultiQC Report (HTML)

    - [P_meandrina/trimmed/multiqc_report.html](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_meandrina/trimmed/multiqc_report.html)

  - FastQs (gzipped)

    - [RNA-POC-47-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_meandrina/trimmed/RNA-POC-47-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz) (3.2G)

      - MD5: `dcc32b44272656f7c0390a157f8d5c87`

    - [RNA-POC-47-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_meandrina/trimmed/RNA-POC-47-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz) (3.3G)

      - MD5: `71d226bb032554d46c861f61dcb708e5`

    - [RNA-POC-48-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_meandrina/trimmed/RNA-POC-48-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz) (3.0G)

      - MD5: `8c8c778d6963789ba3907f42a0749fbe`

    - [RNA-POC-48-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_meandrina/trimmed/RNA-POC-48-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz) (3.1G)

      - MD5: `5d0dadb66923b6d8762ce93905f9ee49`

    - [RNA-POC-50-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_meandrina/trimmed/RNA-POC-50-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz) (3.3G)

      - MD5: `43dcb5cca9ac2f98c7ad94c7bc634e28`

    - [RNA-POC-50-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_meandrina/trimmed/RNA-POC-50-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz) (3.4G)

      - MD5: `577fffdd620cd680ec9ffcfa5a722ae6`

    - [RNA-POC-53-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_meandrina/trimmed/RNA-POC-53-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz) (3.2G)

      - MD5: `766e4544396b2c8abe377434212845e6`

    - [RNA-POC-53-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_meandrina/trimmed/RNA-POC-53-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz) (3.3G)

      - MD5: `a2411c6d56235dd9aff377039d12672a`

    - [RNA-POC-57-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_meandrina/trimmed/RNA-POC-57-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz) (2.5G)

      - MD5: `b3d94288439f57be25f5440a9beccfc0`

    - [RNA-POC-57-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz](https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/P_meandrina/trimmed/RNA-POC-57-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz) (2.6G)

      - MD5: `d0f0d1b29bbeebce67ea22d4bb333988`