FastQC MultiQC - P.tuahiniensis RNA-seq Data for timeseries_molecular Project

2025
Pocillopora tuahiniensis
E5
FastQC
MultiQC
timeseries_molecular
Author

Sam White

Published

February 20, 2025

INTRO

This notebook ran FastQC and MultiQC on the P.evermanni raw RNA-seq data received 20240926 (Notebook), as part of urol-e5/timeseries_molecular (GitHub repo).

Additionally, it renamed the raw FastQs as <species>-<colony_ID>-<timepoint> to allow for easier sample parsing and maintain consistency throughout the project.

Note

The contents below are from markdown knitted from 00.00-F-Ptua-RNAseq-reads-FastQC-MultiQC.md (commit 7d2ba1c).

This Rmd file will download raw RNA-seq FastQs for P.tuahiniensis and evaluate them using FastQC and MultiQC(Ewels et al. 2016).

1 Create a Bash variables file

This allows usage of Bash variables across R Markdown chunks.

{
echo "#### Assign Variables ####"
echo ""

echo "# Data directories"
echo 'export timeseries_dir=/home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular'
echo 'export output_dir_top=${timeseries_dir}/F-Ptua/output/00.00-F-Ptua-RNAseq-reads-FastQC-MultiQC'
echo 'export raw_reads_dir=${timeseries_dir}/F-Ptua/data/rnaseq-raw-fastqs'
echo 'export raw_reads_url="https://owl.fish.washington.edu/nightingales/E5-coral-time-series/30-1047560508/"'
echo ""

echo "# Input files"
echo 'export metadata_file="${timeseries_dir}/M-multi-species/data/rna_metadata.csv"'

echo "# Paths to programs"
echo 'export fastqc=/home/shared/FastQC-0.12.1/fastqc'
echo 'export multiqc=/home/sam/programs/mambaforge/bin/multiqc'
echo ""

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

echo "# Set number of CPUs to use"
echo 'export threads=40'
echo ""


echo "## Inititalize arrays"
echo 'export fastq_array_R1=()'
echo 'export fastq_array_R2=()'
echo 'export raw_fastqs_array=()'
echo 'export R1_names_array=()'
echo 'export R2_names_array=()'
echo ""

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

echo "# Print formatting"
echo 'export line="--------------------------------------------------------"'
echo ""
} > .bashvars

cat .bashvars
#### Assign Variables ####

# Data directories
export timeseries_dir=/home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular
export output_dir_top=${timeseries_dir}/F-Ptua/output/00.00-F-Ptua-RNAseq-reads-FastQC-MultiQC
export raw_reads_dir=${timeseries_dir}/F-Ptua/data/rnaseq-raw-fastqs
export raw_reads_url="https://owl.fish.washington.edu/nightingales/E5-coral-time-series/30-1047560508/"

# Input files
export metadata_file="${timeseries_dir}/M-multi-species/data/rna_metadata.csv"
# Paths to programs
export fastqc=/home/shared/FastQC-0.12.1/fastqc
export multiqc=/home/sam/programs/mambaforge/bin/multiqc

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

# Set number of CPUs to use
export threads=40

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

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

# Print formatting
export line="--------------------------------------------------------"

2 Download P.tuahiniensis RNA-seq FastQs

2.1 Inspect metadata file

# Load bash variables into memory
source .bashvars

head ${metadata_file} |
column -t -s","
SampleNumber  SampleName            Plate  WellNumber  AzentaSampleName  ColonyID  Timepoint  SampleType  Species-Strain    SampleBuffer            TotalAmount-ng  Volume-uL  Conc-ng.uL  PurificationMethod               BiosafetyLevel  MethodUsedForFluorescence  MethodUsedForSpectrophotometry  MethodUsedForElectrophoresis
1             20230123_ACR-225_TP1  1      H11         1H11              ACR-225   TP1        Total RNA   Acropora pulchra  DNAse/RNAse-free water  2529            90         28.1        Column clean-up (Zymo Miniprep)  None            Qubit                      NA                              1.5% TAE agarose non-denaturing gel  Split volume for total RNA (30-1047560508) and small RNA (30-1069297013) sequencing 
2             291-20220211          1      H6          1H6               ACR-225   TP2        Total RNA   Acropora pulchra  DNAse/RNAse-free water  936             90         10.4        Column clean-up (Zymo Miniprep)  None            Qubit                      NA                              1.5% TAE agarose non-denaturing gel  Split volume for total RNA (30-1047560508) and small RNA (30-1069297013) sequencing 
3             527                   1      B1          1B1               ACR-225   TP3        Total RNA   Acropora pulchra  DNAse/RNAse-free water  1722.6          87         19.8        Column clean-up (Zymo Miniprep)  None            Qubit                      NA                              1.5% TAE agarose non-denaturing gel  Split volume for total RNA (30-1047560508) and small RNA (30-1069297013) sequencing 
4             20230123_ACR-225_TP4  1      D3          1D3               ACR-225   TP4        Total RNA   Acropora pulchra  DNAse/RNAse-free water  3168            90         35.2        Column clean-up (Zymo Miniprep)  None            Qubit                      NA                              1.5% TAE agarose non-denaturing gel  Split volume for total RNA (30-1047560508) and small RNA (30-1069297013) sequencing 
5             20230123_ACR-229_TP1  1      B5          1B5               ACR-229   TP1        Total RNA   Acropora pulchra  DNAse/RNAse-free water  4437            90         49.3        Column clean-up (Zymo Miniprep)  None            Qubit                      NA                              1.5% TAE agarose non-denaturing gel  Split volume for total RNA (30-1047560508) and small RNA (30-1069297013) sequencing 
6             295                   1      D6          1D6               ACR-229   TP2        Total RNA   Acropora pulchra  DNAse/RNAse-free water  957             87         11          Column clean-up (Zymo Miniprep)  None            Qubit                      NA                              1.5% TAE agarose non-denaturing gel  Split volume for total RNA (30-1047560508) and small RNA (30-1069297013) sequencing 
7             531                   1      H7          1H7               ACR-229   TP3        Total RNA   Acropora pulchra  DNAse/RNAse-free water  1522.5          87         17.5        Column clean-up (Zymo Miniprep)  None            Qubit                      NA                              1.5% TAE agarose non-denaturing gel  Split volume for total RNA (30-1047560508) and small RNA (30-1069297013) sequencing 
8             20230123_ACR-229_TP4  1      D9          1D9               ACR-229   TP4        Total RNA   Acropora pulchra  DNAse/RNAse-free water  6723            90         74.7        Column clean-up (Zymo Miniprep)  None            Qubit                      NA                              1.5% TAE agarose non-denaturing gel  Split volume for total RNA (30-1047560508) and small RNA (30-1069297013) sequencing 
9             20230123_ACR-237_TP1  1      E9          1E9               ACR-237   TP1        Total RNA   Acropora pulchra  DNAse/RNAse-free water  3744            90         41.6        Column clean-up (Zymo Miniprep)  None            Qubit                      NA                              1.5% TAE agarose non-denaturing gel  Split volume for total RNA (30-1047560508) and small RNA (30-1069297013) sequencing

2.2 Download raw RNA-seq reads

Reads are downloaded from https://owl.fish.washington.edu/nightingales/E5-coral-time-series/30-1047560508/

Since sequencing included multiple species, the code will also parse only those that are P.tuahiniensis.

The --cut-dirs 3 command cuts the preceding directory structure (i.e. nightingales/E5-coral-time-series/30-1047560508/) so that we just end up with the reads.

# Load bash variables into memory
source .bashvars

# Make output directory if it doesn't exist
mkdir --parents ${raw_reads_dir}

# Create list of only P.tuahiniensis sample names
# Extract the AzentaSampleName for P.tuahiniensis samples
sample_list=$(awk -F"," '$9 == "Pocillopora tuahiniensis" { print $5 }' ${timeseries_dir}/M-multi-species/data/rna_metadata.csv | sort)

echo ""
echo "${line}"
echo ""
echo "Sample list:"
echo ""
echo "${sample_list}"
echo ""
echo "${line}"
echo ""

# Use printf to format each item for use in wget
# Add a wildcard to ignore the <number>-- prefix
formatted_list=$(printf "*--%s_*," ${sample_list})

# Remove the trailing comma
formatted_list="${formatted_list%,}"

# Output the final wget command
echo ""
echo "${line}"
echo ""
echo "Formatted wget accept list:"
echo ""
echo "wget --accept=\"$formatted_list\""
echo ""
echo "${line}"
echo ""

# Run wget to retrieve FastQs and MD5 files
# Note: the --no-clobber command will skip re-downloading any files that are already present in the output directory
wget \
--directory-prefix ${raw_reads_dir} \
--recursive \
--no-check-certificate \
--continue \
--cut-dirs 3 \
--no-host-directories \
--no-parent \
--quiet \
--no-clobber \
--accept=${formatted_list} ${raw_reads_url}

ls -lh "${raw_reads_dir}"
--------------------------------------------------------

Sample list:

1A3
1A4
1A5
1A6
1B11
1B12
1B8
1C1
1C2
1C3
1C7
1C8
1C9
1D11
1E10
1E11
1E12
1E4
1E6
1E8
1F2
1F5
1F9
1G11
1G12
1G2
1G4
1G6
1G7
1G8
1G9
1H10
1H4
1H5
1H9
2A1
2A2
2C3
2G2

--------------------------------------------------------


--------------------------------------------------------

Formatted wget accept list:

wget --accept="*--1A3_*,*--1A4_*,*--1A5_*,*--1A6_*,*--1B11_*,*--1B12_*,*--1B8_*,*--1C1_*,*--1C2_*,*--1C3_*,*--1C7_*,*--1C8_*,*--1C9_*,*--1D11_*,*--1E10_*,*--1E11_*,*--1E12_*,*--1E4_*,*--1E6_*,*--1E8_*,*--1F2_*,*--1F5_*,*--1F9_*,*--1G11_*,*--1G12_*,*--1G2_*,*--1G4_*,*--1G6_*,*--1G7_*,*--1G8_*,*--1G9_*,*--1H10_*,*--1H4_*,*--1H5_*,*--1H9_*,*--2A1_*,*--2A2_*,*--2C3_*,*--2G2_*"

--------------------------------------------------------

total 100G
-rw-r--r-- 1 sam sam  1.3G Oct  3 08:53 105--2A2_R1_001.fastq.gz
-rw-r--r-- 1 sam sam    61 Oct  3 08:53 105--2A2_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.4G Oct  3 08:55 105--2A2_R2_001.fastq.gz
-rw-r--r-- 1 sam sam    61 Oct  3 08:55 105--2A2_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.4G Oct  3 09:20 111--2G2_R1_001.fastq.gz
-rw-r--r-- 1 sam sam    61 Oct  3 09:20 111--2G2_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.4G Oct  3 09:22 111--2G2_R2_001.fastq.gz
-rw-r--r-- 1 sam sam    61 Oct  3 09:22 111--2G2_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.1G Oct  3 09:12 11--1C2_R1_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 09:12 11--1C2_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.1G Oct  3 09:14 11--1C2_R2_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 09:14 11--1C2_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.2G Oct  3 09:35 115--2C3_R1_001.fastq.gz
-rw-r--r-- 1 sam sam    61 Oct  3 09:35 115--2C3_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.2G Oct  3 09:37 115--2C3_R2_001.fastq.gz
-rw-r--r-- 1 sam sam    61 Oct  3 09:37 115--2C3_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.3G Oct  3 09:54 14--1F2_R1_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 09:54 14--1F2_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.3G Oct  3 09:55 14--1F2_R2_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 09:55 14--1F2_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.3G Oct  3 09:57 15--1G2_R1_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 09:57 15--1G2_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.3G Oct  3 09:59 15--1G2_R2_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 09:59 15--1G2_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.3G Oct  3 10:04 17--1A3_R1_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 10:04 17--1A3_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.3G Oct  3 10:06 17--1A3_R2_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 10:06 17--1A3_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.5G Oct  3 10:12 19--1C3_R1_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 10:12 19--1C3_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.5G Oct  3 10:14 19--1C3_R2_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 10:14 19--1C3_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.1G Oct  3 10:38 25--1A4_R1_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 10:38 25--1A4_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.1G Oct  3 10:39 25--1A4_R2_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 10:39 25--1A4_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.4G Oct  3 10:53 29--1E4_R1_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 10:53 29--1E4_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.4G Oct  3 10:55 29--1E4_R2_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 10:55 29--1E4_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.5G Oct  3 11:04 31--1G4_R1_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 11:04 31--1G4_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.5G Oct  3 11:06 31--1G4_R2_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 11:06 31--1G4_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.2G Oct  3 10:57 3--1C1_R1_001.fastq.gz
-rw-r--r-- 1 sam sam    59 Oct  3 10:57 3--1C1_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.3G Oct  3 10:58 3--1C1_R2_001.fastq.gz
-rw-r--r-- 1 sam sam    59 Oct  3 10:58 3--1C1_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.5G Oct  3 11:08 32--1H4_R1_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 11:08 32--1H4_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.5G Oct  3 11:11 32--1H4_R2_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 11:11 32--1H4_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.4G Oct  3 11:13 33--1A5_R1_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 11:13 33--1A5_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.4G Oct  3 11:15 33--1A5_R2_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 11:15 33--1A5_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.3G Oct  3 11:32 38--1F5_R1_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 11:32 38--1F5_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.3G Oct  3 11:34 38--1F5_R2_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 11:34 38--1F5_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 1004M Oct  3 11:43 40--1H5_R1_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 11:43 40--1H5_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam 1023M Oct  3 11:44 40--1H5_R2_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 11:44 40--1H5_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.2G Oct  3 11:46 41--1A6_R1_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 11:46 41--1A6_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.2G Oct  3 11:47 41--1A6_R2_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 11:47 41--1A6_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.4G Oct  3 12:00 45--1E6_R1_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 12:00 45--1E6_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.4G Oct  3 12:02 45--1E6_R2_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 12:02 45--1E6_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.3G Oct  3 12:08 47--1G6_R1_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 12:08 47--1G6_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.3G Oct  3 12:10 47--1G6_R2_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 12:10 47--1G6_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.2G Oct  3 12:27 51--1C7_R1_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 12:27 51--1C7_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.2G Oct  3 12:28 51--1C7_R2_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 12:28 51--1C7_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.1G Oct  3 12:41 55--1G7_R1_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 12:41 55--1G7_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.1G Oct  3 12:42 55--1G7_R2_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 12:42 55--1G7_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.3G Oct  3 12:50 58--1B8_R1_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 12:50 58--1B8_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.3G Oct  3 12:52 58--1B8_R2_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 12:52 58--1B8_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.2G Oct  3 12:54 59--1C8_R1_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 12:54 59--1C8_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.2G Oct  3 12:55 59--1C8_R2_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 12:55 59--1C8_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.3G Oct  3 13:04 61--1E8_R1_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 13:04 61--1E8_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.4G Oct  3 13:06 61--1E8_R2_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 13:06 61--1E8_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.4G Oct  3 13:13 63--1G8_R1_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 13:13 63--1G8_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.5G Oct  3 13:15 63--1G8_R2_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 13:15 63--1G8_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.3G Oct  3 13:29 67--1C9_R1_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 13:29 67--1C9_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.3G Oct  3 13:31 67--1C9_R2_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 13:31 67--1C9_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.4G Oct  3 13:45 70--1F9_R1_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 13:45 70--1F9_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.4G Oct  3 13:47 70--1F9_R2_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 13:47 70--1F9_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.2G Oct  3 13:49 71--1G9_R1_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 13:49 71--1G9_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.2G Oct  3 13:50 71--1G9_R2_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 13:50 71--1G9_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.3G Oct  3 13:52 72--1H9_R1_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 13:52 72--1H9_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.3G Oct  3 13:54 72--1H9_R2_001.fastq.gz
-rw-r--r-- 1 sam sam    60 Oct  3 13:54 72--1H9_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.4G Oct  3 14:11 77--1E10_R1_001.fastq.gz
-rw-r--r-- 1 sam sam    61 Oct  3 14:11 77--1E10_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.4G Oct  3 14:13 77--1E10_R2_001.fastq.gz
-rw-r--r-- 1 sam sam    61 Oct  3 14:13 77--1E10_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  1.5G Oct  3 14:25 80--1H10_R1_001.fastq.gz
-rw-r--r-- 1 sam sam    61 Oct  3 14:25 80--1H10_R1_001.fastq.gz.md5
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-rw-r--r-- 1 sam sam  1.4G Oct  3 14:45 85--1E11_R2_001.fastq.gz
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-rw-r--r-- 1 sam sam  1.5G Oct  3 15:04 90--1B12_R1_001.fastq.gz
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-rw-r--r-- 1 sam sam  1.3G Oct  3 15:31 97--2A1_R1_001.fastq.gz
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3 Rename FastQs

# Load bash variables into memory
source .bashvars

cd "${raw_reads_dir}"

# Create an associative array to store the mapping
declare -A azenta_to_colony_timepoint

# Create a temporary file to store the mapping
temp_mapping_file=$(mktemp)

# Read the metadata file and populate the temporary file using awk
# Maps Azenta sample name to colony_id and timepoint.
awk -F, 'NR > 1 { print $5, $6 "-" $7 }' "$metadata_file" > "$temp_mapping_file"

# Read the temporary file and populate the associative array
while read -r azenta_sample_name colony_timepoint; do
    azenta_to_colony_timepoint["$azenta_sample_name"]="$colony_timepoint"
done < "$temp_mapping_file"

# Remove the temporary file
rm "$temp_mapping_file"

# Print the associative array for debugging
echo "Azenta sample name to colony_id-Timepoint mapping:"
for key in "${!azenta_to_colony_timepoint[@]}"; do
    echo ""
    echo "$key -> ${azenta_to_colony_timepoint[$key]}"
    echo ""
done

# Iterate over the FastQ files in the current directory
for fastq_file in *.fastq.gz *.md5; do
    # Extract the Azenta sample name from the filename
    azenta_sample_name=$(echo "$fastq_file" | sed -E 's/^[0-9]+--([A-Za-z0-9]+)_.*/\1/')
    
    # Check if the Azenta sample name exists in the associative array
    if [[ -n "${azenta_to_colony_timepoint[$azenta_sample_name]}" ]]; then
        new_sample_name="${azenta_to_colony_timepoint[$azenta_sample_name]}"
        new_filename=$(echo "$fastq_file" | sed -E "s/^[0-9]+--$azenta_sample_name/$new_sample_name/")
        if [[ "$fastq_file" != "$new_filename" ]]; then
            mv "$fastq_file" "$new_filename"
            echo "Renamed $fastq_file to $new_filename"
        else
            echo "No renaming needed for $fastq_file"
        fi

        # If the file is a .md5 file, update its contents
        if [[ "$fastq_file" == *.md5 ]]; then
            sed -i -E "s|(\./)[0-9]+--$azenta_sample_name|\1$new_sample_name|" "$new_filename"
            echo "Updated contents of $new_filename"
            echo ""
        fi
    else
        echo "Azenta sample name '$azenta_sample_name' not found in metadata."
        # Debugging: Print all keys in the associative array with quotes
        echo "Available keys in the associative array:"
        for key in "${!azenta_to_colony_timepoint[@]}"; do
            echo "'$key'"
        done
    fi
done
Azenta sample name to colony_id-Timepoint mapping:

1B3 -> POR-83-TP3


1B2 -> ACR-173-TP3


1B1 -> ACR-225-TP3


1B7 -> POR-245-TP2


1B6 -> POR-260-TP4


1B5 -> ACR-229-TP1


1B4 -> POR-72-TP1


1B9 -> ACR-265-TP4


1B8 -> POC-201-TP1


1D5 -> POR-260-TP1


1C1 -> POC-57-TP2


1D4 -> ACR-237-TP4


1D7 -> POR-74-TP1


1C2 -> POC-222-TP4


1C3 -> POC-222-TP3


1D6 -> ACR-229-TP2


1D1 -> POR-245-TP4


1B12 -> POC-222-TP2


1C4 -> ACR-139-TP4


1C5 -> POR-73-TP3


1C6 -> POR-262-TP2


1B10 -> ACR-150-TP4


1D3 -> ACR-225-TP4


1D2 -> POR-245-TP1


1C7 -> POC-52-TP4


1B11 -> POC-40-TP1


1C8 -> POC-42-TP1


1C9 -> POC-222-TP1


2C3 -> POC-57-TP1


1D9 -> ACR-229-TP4


2C2 -> ACR-139-TP1


1D8 -> ACR-237-TP2


2C1 -> ACR-244-TP1


1E2 -> POR-69-TP3


1E3 -> ACR-150-TP2


1E1 -> ACR-265-TP3


1E6 -> POC-40-TP3


1E7 -> POR-69-TP4


1E4 -> POC-259-TP2


1E5 -> ACR-139-TP3


1E11 -> POC-219-TP1


1E10 -> POC-40-TP2


1E8 -> POC-42-TP3


1E12 -> POC-255-TP4


1E9 -> ACR-237-TP1


2B1 -> POR-72-TP2


2B2 -> ACR-145-TP1


2B3 -> ACR-139-TP2


2E1 -> POR-216-TP3


2E3 -> POR-236-TP2


2E2 -> ACR-186-TP1


1H1 -> POR-245-TP3


1H3 -> POR-83-TP1


1H2 -> POR-73-TP4


1H5 -> POC-201-TP3


2D2 -> ACR-150-TP1


2D3 -> POR-262-TP3


1H4 -> POC-42-TP2


1F9 -> POC-52-TP2


1H7 -> ACR-229-TP3


2D1 -> POR-236-TP1


1F8 -> ACR-145-TP3


1H6 -> ACR-225-TP2


1F7 -> POR-83-TP4


1H9 -> POC-53-TP4


1F6 -> POR-69-TP1


1H8 -> ACR-186-TP4


1F5 -> POC-40-TP4


1F4 -> ACR-150-TP3


1F3 -> POR-83-TP2


1D10 -> ACR-265-TP2


1F2 -> POC-259-TP4


1D11 -> POC-255-TP3


1F1 -> POR-73-TP2


1D12 -> POR-260-TP2


2G2 -> POC-57-TP4


2G1 -> ACR-145-TP2


1G8 -> POC-259-TP3


1G9 -> POC-259-TP1


1G12 -> POC-219-TP4


1G11 -> POC-53-TP1


1G10 -> POR-74-TP2


1G4 -> POC-57-TP3


1G5 -> ACR-244-TP3


1G6 -> POC-53-TP2


1G7 -> POC-42-TP4


1G1 -> POR-262-TP1


1G2 -> POC-219-TP3


1G3 -> POR-74-TP3


2F1 -> ACR-265-TP1


2F2 -> POR-216-TP4


1A11 -> POR-216-TP2


2A1 -> POC-219-TP2


1A10 -> ACR-145-TP4


2A3 -> POR-262-TP4


2A2 -> POC-255-TP2


1A12 -> ACR-237-TP3


2H2 -> POR-216-TP1


2H1 -> POR-69-TP2


1A6 -> POC-52-TP3


1H10 -> POC-201-TP2


1A7 -> POR-73-TP1


1C12 -> POR-72-TP3


1H11 -> ACR-225-TP1


1C11 -> POR-74-TP4


1A4 -> POC-52-TP1


1H12 -> ACR-186-TP3


1A5 -> POC-53-TP3


1C10 -> ACR-173-TP4


1A2 -> ACR-244-TP4


1A3 -> POC-255-TP1


1A1 -> ACR-173-TP1


1F12 -> POR-72-TP4


1F10 -> POR-260-TP3


1F11 -> ACR-173-TP2


1A8 -> ACR-186-TP2


1A9 -> ACR-244-TP2

Renamed 105--2A2_R1_001.fastq.gz to POC-255-TP2_R1_001.fastq.gz
Renamed 105--2A2_R2_001.fastq.gz to POC-255-TP2_R2_001.fastq.gz
Renamed 111--2G2_R1_001.fastq.gz to POC-57-TP4_R1_001.fastq.gz
Renamed 111--2G2_R2_001.fastq.gz to POC-57-TP4_R2_001.fastq.gz
Renamed 11--1C2_R1_001.fastq.gz to POC-222-TP4_R1_001.fastq.gz
Renamed 11--1C2_R2_001.fastq.gz to POC-222-TP4_R2_001.fastq.gz
Renamed 115--2C3_R1_001.fastq.gz to POC-57-TP1_R1_001.fastq.gz
Renamed 115--2C3_R2_001.fastq.gz to POC-57-TP1_R2_001.fastq.gz
Renamed 14--1F2_R1_001.fastq.gz to POC-259-TP4_R1_001.fastq.gz
Renamed 14--1F2_R2_001.fastq.gz to POC-259-TP4_R2_001.fastq.gz
Renamed 15--1G2_R1_001.fastq.gz to POC-219-TP3_R1_001.fastq.gz
Renamed 15--1G2_R2_001.fastq.gz to POC-219-TP3_R2_001.fastq.gz
Renamed 17--1A3_R1_001.fastq.gz to POC-255-TP1_R1_001.fastq.gz
Renamed 17--1A3_R2_001.fastq.gz to POC-255-TP1_R2_001.fastq.gz
Renamed 19--1C3_R1_001.fastq.gz to POC-222-TP3_R1_001.fastq.gz
Renamed 19--1C3_R2_001.fastq.gz to POC-222-TP3_R2_001.fastq.gz
Renamed 25--1A4_R1_001.fastq.gz to POC-52-TP1_R1_001.fastq.gz
Renamed 25--1A4_R2_001.fastq.gz to POC-52-TP1_R2_001.fastq.gz
Renamed 29--1E4_R1_001.fastq.gz to POC-259-TP2_R1_001.fastq.gz
Renamed 29--1E4_R2_001.fastq.gz to POC-259-TP2_R2_001.fastq.gz
Renamed 31--1G4_R1_001.fastq.gz to POC-57-TP3_R1_001.fastq.gz
Renamed 31--1G4_R2_001.fastq.gz to POC-57-TP3_R2_001.fastq.gz
Renamed 3--1C1_R1_001.fastq.gz to POC-57-TP2_R1_001.fastq.gz
Renamed 3--1C1_R2_001.fastq.gz to POC-57-TP2_R2_001.fastq.gz
Renamed 32--1H4_R1_001.fastq.gz to POC-42-TP2_R1_001.fastq.gz
Renamed 32--1H4_R2_001.fastq.gz to POC-42-TP2_R2_001.fastq.gz
Renamed 33--1A5_R1_001.fastq.gz to POC-53-TP3_R1_001.fastq.gz
Renamed 33--1A5_R2_001.fastq.gz to POC-53-TP3_R2_001.fastq.gz
Renamed 38--1F5_R1_001.fastq.gz to POC-40-TP4_R1_001.fastq.gz
Renamed 38--1F5_R2_001.fastq.gz to POC-40-TP4_R2_001.fastq.gz
Renamed 40--1H5_R1_001.fastq.gz to POC-201-TP3_R1_001.fastq.gz
Renamed 40--1H5_R2_001.fastq.gz to POC-201-TP3_R2_001.fastq.gz
Renamed 41--1A6_R1_001.fastq.gz to POC-52-TP3_R1_001.fastq.gz
Renamed 41--1A6_R2_001.fastq.gz to POC-52-TP3_R2_001.fastq.gz
Renamed 45--1E6_R1_001.fastq.gz to POC-40-TP3_R1_001.fastq.gz
Renamed 45--1E6_R2_001.fastq.gz to POC-40-TP3_R2_001.fastq.gz
Renamed 47--1G6_R1_001.fastq.gz to POC-53-TP2_R1_001.fastq.gz
Renamed 47--1G6_R2_001.fastq.gz to POC-53-TP2_R2_001.fastq.gz
Renamed 51--1C7_R1_001.fastq.gz to POC-52-TP4_R1_001.fastq.gz
Renamed 51--1C7_R2_001.fastq.gz to POC-52-TP4_R2_001.fastq.gz
Renamed 55--1G7_R1_001.fastq.gz to POC-42-TP4_R1_001.fastq.gz
Renamed 55--1G7_R2_001.fastq.gz to POC-42-TP4_R2_001.fastq.gz
Renamed 58--1B8_R1_001.fastq.gz to POC-201-TP1_R1_001.fastq.gz
Renamed 58--1B8_R2_001.fastq.gz to POC-201-TP1_R2_001.fastq.gz
Renamed 59--1C8_R1_001.fastq.gz to POC-42-TP1_R1_001.fastq.gz
Renamed 59--1C8_R2_001.fastq.gz to POC-42-TP1_R2_001.fastq.gz
Renamed 61--1E8_R1_001.fastq.gz to POC-42-TP3_R1_001.fastq.gz
Renamed 61--1E8_R2_001.fastq.gz to POC-42-TP3_R2_001.fastq.gz
Renamed 63--1G8_R1_001.fastq.gz to POC-259-TP3_R1_001.fastq.gz
Renamed 63--1G8_R2_001.fastq.gz to POC-259-TP3_R2_001.fastq.gz
Renamed 67--1C9_R1_001.fastq.gz to POC-222-TP1_R1_001.fastq.gz
Renamed 67--1C9_R2_001.fastq.gz to POC-222-TP1_R2_001.fastq.gz
Renamed 70--1F9_R1_001.fastq.gz to POC-52-TP2_R1_001.fastq.gz
Renamed 70--1F9_R2_001.fastq.gz to POC-52-TP2_R2_001.fastq.gz
Renamed 71--1G9_R1_001.fastq.gz to POC-259-TP1_R1_001.fastq.gz
Renamed 71--1G9_R2_001.fastq.gz to POC-259-TP1_R2_001.fastq.gz
Renamed 72--1H9_R1_001.fastq.gz to POC-53-TP4_R1_001.fastq.gz
Renamed 72--1H9_R2_001.fastq.gz to POC-53-TP4_R2_001.fastq.gz
Renamed 77--1E10_R1_001.fastq.gz to POC-40-TP2_R1_001.fastq.gz
Renamed 77--1E10_R2_001.fastq.gz to POC-40-TP2_R2_001.fastq.gz
Renamed 80--1H10_R1_001.fastq.gz to POC-201-TP2_R1_001.fastq.gz
Renamed 80--1H10_R2_001.fastq.gz to POC-201-TP2_R2_001.fastq.gz
Renamed 82--1B11_R1_001.fastq.gz to POC-40-TP1_R1_001.fastq.gz
Renamed 82--1B11_R2_001.fastq.gz to POC-40-TP1_R2_001.fastq.gz
Renamed 84--1D11_R1_001.fastq.gz to POC-255-TP3_R1_001.fastq.gz
Renamed 84--1D11_R2_001.fastq.gz to POC-255-TP3_R2_001.fastq.gz
Renamed 85--1E11_R1_001.fastq.gz to POC-219-TP1_R1_001.fastq.gz
Renamed 85--1E11_R2_001.fastq.gz to POC-219-TP1_R2_001.fastq.gz
Renamed 87--1G11_R1_001.fastq.gz to POC-53-TP1_R1_001.fastq.gz
Renamed 87--1G11_R2_001.fastq.gz to POC-53-TP1_R2_001.fastq.gz
Renamed 90--1B12_R1_001.fastq.gz to POC-222-TP2_R1_001.fastq.gz
Renamed 90--1B12_R2_001.fastq.gz to POC-222-TP2_R2_001.fastq.gz
Renamed 93--1E12_R1_001.fastq.gz to POC-255-TP4_R1_001.fastq.gz
Renamed 93--1E12_R2_001.fastq.gz to POC-255-TP4_R2_001.fastq.gz
Renamed 95--1G12_R1_001.fastq.gz to POC-219-TP4_R1_001.fastq.gz
Renamed 95--1G12_R2_001.fastq.gz to POC-219-TP4_R2_001.fastq.gz
Renamed 97--2A1_R1_001.fastq.gz to POC-219-TP2_R1_001.fastq.gz
Renamed 97--2A1_R2_001.fastq.gz to POC-219-TP2_R2_001.fastq.gz
Renamed 105--2A2_R1_001.fastq.gz.md5 to POC-255-TP2_R1_001.fastq.gz.md5
Updated contents of POC-255-TP2_R1_001.fastq.gz.md5

Renamed 105--2A2_R2_001.fastq.gz.md5 to POC-255-TP2_R2_001.fastq.gz.md5
Updated contents of POC-255-TP2_R2_001.fastq.gz.md5

Renamed 111--2G2_R1_001.fastq.gz.md5 to POC-57-TP4_R1_001.fastq.gz.md5
Updated contents of POC-57-TP4_R1_001.fastq.gz.md5

Renamed 111--2G2_R2_001.fastq.gz.md5 to POC-57-TP4_R2_001.fastq.gz.md5
Updated contents of POC-57-TP4_R2_001.fastq.gz.md5

Renamed 11--1C2_R1_001.fastq.gz.md5 to POC-222-TP4_R1_001.fastq.gz.md5
Updated contents of POC-222-TP4_R1_001.fastq.gz.md5

Renamed 11--1C2_R2_001.fastq.gz.md5 to POC-222-TP4_R2_001.fastq.gz.md5
Updated contents of POC-222-TP4_R2_001.fastq.gz.md5

Renamed 115--2C3_R1_001.fastq.gz.md5 to POC-57-TP1_R1_001.fastq.gz.md5
Updated contents of POC-57-TP1_R1_001.fastq.gz.md5

Renamed 115--2C3_R2_001.fastq.gz.md5 to POC-57-TP1_R2_001.fastq.gz.md5
Updated contents of POC-57-TP1_R2_001.fastq.gz.md5

Renamed 14--1F2_R1_001.fastq.gz.md5 to POC-259-TP4_R1_001.fastq.gz.md5
Updated contents of POC-259-TP4_R1_001.fastq.gz.md5

Renamed 14--1F2_R2_001.fastq.gz.md5 to POC-259-TP4_R2_001.fastq.gz.md5
Updated contents of POC-259-TP4_R2_001.fastq.gz.md5

Renamed 15--1G2_R1_001.fastq.gz.md5 to POC-219-TP3_R1_001.fastq.gz.md5
Updated contents of POC-219-TP3_R1_001.fastq.gz.md5

Renamed 15--1G2_R2_001.fastq.gz.md5 to POC-219-TP3_R2_001.fastq.gz.md5
Updated contents of POC-219-TP3_R2_001.fastq.gz.md5

Renamed 17--1A3_R1_001.fastq.gz.md5 to POC-255-TP1_R1_001.fastq.gz.md5
Updated contents of POC-255-TP1_R1_001.fastq.gz.md5

Renamed 17--1A3_R2_001.fastq.gz.md5 to POC-255-TP1_R2_001.fastq.gz.md5
Updated contents of POC-255-TP1_R2_001.fastq.gz.md5

Renamed 19--1C3_R1_001.fastq.gz.md5 to POC-222-TP3_R1_001.fastq.gz.md5
Updated contents of POC-222-TP3_R1_001.fastq.gz.md5

Renamed 19--1C3_R2_001.fastq.gz.md5 to POC-222-TP3_R2_001.fastq.gz.md5
Updated contents of POC-222-TP3_R2_001.fastq.gz.md5

Renamed 25--1A4_R1_001.fastq.gz.md5 to POC-52-TP1_R1_001.fastq.gz.md5
Updated contents of POC-52-TP1_R1_001.fastq.gz.md5

Renamed 25--1A4_R2_001.fastq.gz.md5 to POC-52-TP1_R2_001.fastq.gz.md5
Updated contents of POC-52-TP1_R2_001.fastq.gz.md5

Renamed 29--1E4_R1_001.fastq.gz.md5 to POC-259-TP2_R1_001.fastq.gz.md5
Updated contents of POC-259-TP2_R1_001.fastq.gz.md5

Renamed 29--1E4_R2_001.fastq.gz.md5 to POC-259-TP2_R2_001.fastq.gz.md5
Updated contents of POC-259-TP2_R2_001.fastq.gz.md5

Renamed 31--1G4_R1_001.fastq.gz.md5 to POC-57-TP3_R1_001.fastq.gz.md5
Updated contents of POC-57-TP3_R1_001.fastq.gz.md5

Renamed 31--1G4_R2_001.fastq.gz.md5 to POC-57-TP3_R2_001.fastq.gz.md5
Updated contents of POC-57-TP3_R2_001.fastq.gz.md5

Renamed 3--1C1_R1_001.fastq.gz.md5 to POC-57-TP2_R1_001.fastq.gz.md5
Updated contents of POC-57-TP2_R1_001.fastq.gz.md5

Renamed 3--1C1_R2_001.fastq.gz.md5 to POC-57-TP2_R2_001.fastq.gz.md5
Updated contents of POC-57-TP2_R2_001.fastq.gz.md5

Renamed 32--1H4_R1_001.fastq.gz.md5 to POC-42-TP2_R1_001.fastq.gz.md5
Updated contents of POC-42-TP2_R1_001.fastq.gz.md5

Renamed 32--1H4_R2_001.fastq.gz.md5 to POC-42-TP2_R2_001.fastq.gz.md5
Updated contents of POC-42-TP2_R2_001.fastq.gz.md5

Renamed 33--1A5_R1_001.fastq.gz.md5 to POC-53-TP3_R1_001.fastq.gz.md5
Updated contents of POC-53-TP3_R1_001.fastq.gz.md5

Renamed 33--1A5_R2_001.fastq.gz.md5 to POC-53-TP3_R2_001.fastq.gz.md5
Updated contents of POC-53-TP3_R2_001.fastq.gz.md5

Renamed 38--1F5_R1_001.fastq.gz.md5 to POC-40-TP4_R1_001.fastq.gz.md5
Updated contents of POC-40-TP4_R1_001.fastq.gz.md5

Renamed 38--1F5_R2_001.fastq.gz.md5 to POC-40-TP4_R2_001.fastq.gz.md5
Updated contents of POC-40-TP4_R2_001.fastq.gz.md5

Renamed 40--1H5_R1_001.fastq.gz.md5 to POC-201-TP3_R1_001.fastq.gz.md5
Updated contents of POC-201-TP3_R1_001.fastq.gz.md5

Renamed 40--1H5_R2_001.fastq.gz.md5 to POC-201-TP3_R2_001.fastq.gz.md5
Updated contents of POC-201-TP3_R2_001.fastq.gz.md5

Renamed 41--1A6_R1_001.fastq.gz.md5 to POC-52-TP3_R1_001.fastq.gz.md5
Updated contents of POC-52-TP3_R1_001.fastq.gz.md5

Renamed 41--1A6_R2_001.fastq.gz.md5 to POC-52-TP3_R2_001.fastq.gz.md5
Updated contents of POC-52-TP3_R2_001.fastq.gz.md5

Renamed 45--1E6_R1_001.fastq.gz.md5 to POC-40-TP3_R1_001.fastq.gz.md5
Updated contents of POC-40-TP3_R1_001.fastq.gz.md5

Renamed 45--1E6_R2_001.fastq.gz.md5 to POC-40-TP3_R2_001.fastq.gz.md5
Updated contents of POC-40-TP3_R2_001.fastq.gz.md5

Renamed 47--1G6_R1_001.fastq.gz.md5 to POC-53-TP2_R1_001.fastq.gz.md5
Updated contents of POC-53-TP2_R1_001.fastq.gz.md5

Renamed 47--1G6_R2_001.fastq.gz.md5 to POC-53-TP2_R2_001.fastq.gz.md5
Updated contents of POC-53-TP2_R2_001.fastq.gz.md5

Renamed 51--1C7_R1_001.fastq.gz.md5 to POC-52-TP4_R1_001.fastq.gz.md5
Updated contents of POC-52-TP4_R1_001.fastq.gz.md5

Renamed 51--1C7_R2_001.fastq.gz.md5 to POC-52-TP4_R2_001.fastq.gz.md5
Updated contents of POC-52-TP4_R2_001.fastq.gz.md5

Renamed 55--1G7_R1_001.fastq.gz.md5 to POC-42-TP4_R1_001.fastq.gz.md5
Updated contents of POC-42-TP4_R1_001.fastq.gz.md5

Renamed 55--1G7_R2_001.fastq.gz.md5 to POC-42-TP4_R2_001.fastq.gz.md5
Updated contents of POC-42-TP4_R2_001.fastq.gz.md5

Renamed 58--1B8_R1_001.fastq.gz.md5 to POC-201-TP1_R1_001.fastq.gz.md5
Updated contents of POC-201-TP1_R1_001.fastq.gz.md5

Renamed 58--1B8_R2_001.fastq.gz.md5 to POC-201-TP1_R2_001.fastq.gz.md5
Updated contents of POC-201-TP1_R2_001.fastq.gz.md5

Renamed 59--1C8_R1_001.fastq.gz.md5 to POC-42-TP1_R1_001.fastq.gz.md5
Updated contents of POC-42-TP1_R1_001.fastq.gz.md5

Renamed 59--1C8_R2_001.fastq.gz.md5 to POC-42-TP1_R2_001.fastq.gz.md5
Updated contents of POC-42-TP1_R2_001.fastq.gz.md5

Renamed 61--1E8_R1_001.fastq.gz.md5 to POC-42-TP3_R1_001.fastq.gz.md5
Updated contents of POC-42-TP3_R1_001.fastq.gz.md5

Renamed 61--1E8_R2_001.fastq.gz.md5 to POC-42-TP3_R2_001.fastq.gz.md5
Updated contents of POC-42-TP3_R2_001.fastq.gz.md5

Renamed 63--1G8_R1_001.fastq.gz.md5 to POC-259-TP3_R1_001.fastq.gz.md5
Updated contents of POC-259-TP3_R1_001.fastq.gz.md5

Renamed 63--1G8_R2_001.fastq.gz.md5 to POC-259-TP3_R2_001.fastq.gz.md5
Updated contents of POC-259-TP3_R2_001.fastq.gz.md5

Renamed 67--1C9_R1_001.fastq.gz.md5 to POC-222-TP1_R1_001.fastq.gz.md5
Updated contents of POC-222-TP1_R1_001.fastq.gz.md5

Renamed 67--1C9_R2_001.fastq.gz.md5 to POC-222-TP1_R2_001.fastq.gz.md5
Updated contents of POC-222-TP1_R2_001.fastq.gz.md5

Renamed 70--1F9_R1_001.fastq.gz.md5 to POC-52-TP2_R1_001.fastq.gz.md5
Updated contents of POC-52-TP2_R1_001.fastq.gz.md5

Renamed 70--1F9_R2_001.fastq.gz.md5 to POC-52-TP2_R2_001.fastq.gz.md5
Updated contents of POC-52-TP2_R2_001.fastq.gz.md5

Renamed 71--1G9_R1_001.fastq.gz.md5 to POC-259-TP1_R1_001.fastq.gz.md5
Updated contents of POC-259-TP1_R1_001.fastq.gz.md5

Renamed 71--1G9_R2_001.fastq.gz.md5 to POC-259-TP1_R2_001.fastq.gz.md5
Updated contents of POC-259-TP1_R2_001.fastq.gz.md5

Renamed 72--1H9_R1_001.fastq.gz.md5 to POC-53-TP4_R1_001.fastq.gz.md5
Updated contents of POC-53-TP4_R1_001.fastq.gz.md5

Renamed 72--1H9_R2_001.fastq.gz.md5 to POC-53-TP4_R2_001.fastq.gz.md5
Updated contents of POC-53-TP4_R2_001.fastq.gz.md5

Renamed 77--1E10_R1_001.fastq.gz.md5 to POC-40-TP2_R1_001.fastq.gz.md5
Updated contents of POC-40-TP2_R1_001.fastq.gz.md5

Renamed 77--1E10_R2_001.fastq.gz.md5 to POC-40-TP2_R2_001.fastq.gz.md5
Updated contents of POC-40-TP2_R2_001.fastq.gz.md5

Renamed 80--1H10_R1_001.fastq.gz.md5 to POC-201-TP2_R1_001.fastq.gz.md5
Updated contents of POC-201-TP2_R1_001.fastq.gz.md5

Renamed 80--1H10_R2_001.fastq.gz.md5 to POC-201-TP2_R2_001.fastq.gz.md5
Updated contents of POC-201-TP2_R2_001.fastq.gz.md5

Renamed 82--1B11_R1_001.fastq.gz.md5 to POC-40-TP1_R1_001.fastq.gz.md5
Updated contents of POC-40-TP1_R1_001.fastq.gz.md5

Renamed 82--1B11_R2_001.fastq.gz.md5 to POC-40-TP1_R2_001.fastq.gz.md5
Updated contents of POC-40-TP1_R2_001.fastq.gz.md5

Renamed 84--1D11_R1_001.fastq.gz.md5 to POC-255-TP3_R1_001.fastq.gz.md5
Updated contents of POC-255-TP3_R1_001.fastq.gz.md5

Renamed 84--1D11_R2_001.fastq.gz.md5 to POC-255-TP3_R2_001.fastq.gz.md5
Updated contents of POC-255-TP3_R2_001.fastq.gz.md5

Renamed 85--1E11_R1_001.fastq.gz.md5 to POC-219-TP1_R1_001.fastq.gz.md5
Updated contents of POC-219-TP1_R1_001.fastq.gz.md5

Renamed 85--1E11_R2_001.fastq.gz.md5 to POC-219-TP1_R2_001.fastq.gz.md5
Updated contents of POC-219-TP1_R2_001.fastq.gz.md5

Renamed 87--1G11_R1_001.fastq.gz.md5 to POC-53-TP1_R1_001.fastq.gz.md5
Updated contents of POC-53-TP1_R1_001.fastq.gz.md5

Renamed 87--1G11_R2_001.fastq.gz.md5 to POC-53-TP1_R2_001.fastq.gz.md5
Updated contents of POC-53-TP1_R2_001.fastq.gz.md5

Renamed 90--1B12_R1_001.fastq.gz.md5 to POC-222-TP2_R1_001.fastq.gz.md5
Updated contents of POC-222-TP2_R1_001.fastq.gz.md5

Renamed 90--1B12_R2_001.fastq.gz.md5 to POC-222-TP2_R2_001.fastq.gz.md5
Updated contents of POC-222-TP2_R2_001.fastq.gz.md5

Renamed 93--1E12_R1_001.fastq.gz.md5 to POC-255-TP4_R1_001.fastq.gz.md5
Updated contents of POC-255-TP4_R1_001.fastq.gz.md5

Renamed 93--1E12_R2_001.fastq.gz.md5 to POC-255-TP4_R2_001.fastq.gz.md5
Updated contents of POC-255-TP4_R2_001.fastq.gz.md5

Renamed 95--1G12_R1_001.fastq.gz.md5 to POC-219-TP4_R1_001.fastq.gz.md5
Updated contents of POC-219-TP4_R1_001.fastq.gz.md5

Renamed 95--1G12_R2_001.fastq.gz.md5 to POC-219-TP4_R2_001.fastq.gz.md5
Updated contents of POC-219-TP4_R2_001.fastq.gz.md5

Renamed 97--2A1_R1_001.fastq.gz.md5 to POC-219-TP2_R1_001.fastq.gz.md5
Updated contents of POC-219-TP2_R1_001.fastq.gz.md5

Renamed 97--2A1_R2_001.fastq.gz.md5 to POC-219-TP2_R2_001.fastq.gz.md5
Updated contents of POC-219-TP2_R2_001.fastq.gz.md5

3.1 Verify raw read checksums

# Load bash variables into memory
source .bashvars

cd "${raw_reads_dir}"

# Checksums file contains other files, so this just looks for the RNAseq files.
for file in *.md5
do
  md5sum --check "${file}"
done
./POC-201-TP1_R1_001.fastq.gz: OK
./POC-201-TP1_R2_001.fastq.gz: OK
./POC-201-TP2_R1_001.fastq.gz: OK
./POC-201-TP2_R2_001.fastq.gz: OK
./POC-201-TP3_R1_001.fastq.gz: OK
./POC-201-TP3_R2_001.fastq.gz: OK
./POC-219-TP1_R1_001.fastq.gz: OK
./POC-219-TP1_R2_001.fastq.gz: OK
./POC-219-TP2_R1_001.fastq.gz: OK
./POC-219-TP2_R2_001.fastq.gz: OK
./POC-219-TP3_R1_001.fastq.gz: OK
./POC-219-TP3_R2_001.fastq.gz: OK
./POC-219-TP4_R1_001.fastq.gz: OK
./POC-219-TP4_R2_001.fastq.gz: OK
./POC-222-TP1_R1_001.fastq.gz: OK
./POC-222-TP1_R2_001.fastq.gz: OK
./POC-222-TP2_R1_001.fastq.gz: OK
./POC-222-TP2_R2_001.fastq.gz: OK
./POC-222-TP3_R1_001.fastq.gz: OK
./POC-222-TP3_R2_001.fastq.gz: OK
./POC-222-TP4_R1_001.fastq.gz: OK
./POC-222-TP4_R2_001.fastq.gz: OK
./POC-255-TP1_R1_001.fastq.gz: OK
./POC-255-TP1_R2_001.fastq.gz: OK
./POC-255-TP2_R1_001.fastq.gz: OK
./POC-255-TP2_R2_001.fastq.gz: OK
./POC-255-TP3_R1_001.fastq.gz: OK
./POC-255-TP3_R2_001.fastq.gz: OK
./POC-255-TP4_R1_001.fastq.gz: OK
./POC-255-TP4_R2_001.fastq.gz: OK
./POC-259-TP1_R1_001.fastq.gz: OK
./POC-259-TP1_R2_001.fastq.gz: OK
./POC-259-TP2_R1_001.fastq.gz: OK
./POC-259-TP2_R2_001.fastq.gz: OK
./POC-259-TP3_R1_001.fastq.gz: OK
./POC-259-TP3_R2_001.fastq.gz: OK
./POC-259-TP4_R1_001.fastq.gz: OK
./POC-259-TP4_R2_001.fastq.gz: OK
./POC-40-TP1_R1_001.fastq.gz: OK
./POC-40-TP1_R2_001.fastq.gz: OK
./POC-40-TP2_R1_001.fastq.gz: OK
./POC-40-TP2_R2_001.fastq.gz: OK
./POC-40-TP3_R1_001.fastq.gz: OK
./POC-40-TP3_R2_001.fastq.gz: OK
./POC-40-TP4_R1_001.fastq.gz: OK
./POC-40-TP4_R2_001.fastq.gz: OK
./POC-42-TP1_R1_001.fastq.gz: OK
./POC-42-TP1_R2_001.fastq.gz: OK
./POC-42-TP2_R1_001.fastq.gz: OK
./POC-42-TP2_R2_001.fastq.gz: OK
./POC-42-TP3_R1_001.fastq.gz: OK
./POC-42-TP3_R2_001.fastq.gz: OK
./POC-42-TP4_R1_001.fastq.gz: OK
./POC-42-TP4_R2_001.fastq.gz: OK
./POC-52-TP1_R1_001.fastq.gz: OK
./POC-52-TP1_R2_001.fastq.gz: OK
./POC-52-TP2_R1_001.fastq.gz: OK
./POC-52-TP2_R2_001.fastq.gz: OK
./POC-52-TP3_R1_001.fastq.gz: OK
./POC-52-TP3_R2_001.fastq.gz: OK
./POC-52-TP4_R1_001.fastq.gz: OK
./POC-52-TP4_R2_001.fastq.gz: OK
./POC-53-TP1_R1_001.fastq.gz: OK
./POC-53-TP1_R2_001.fastq.gz: OK
./POC-53-TP2_R1_001.fastq.gz: OK
./POC-53-TP2_R2_001.fastq.gz: OK
./POC-53-TP3_R1_001.fastq.gz: OK
./POC-53-TP3_R2_001.fastq.gz: OK
./POC-53-TP4_R1_001.fastq.gz: OK
./POC-53-TP4_R2_001.fastq.gz: OK
./POC-57-TP1_R1_001.fastq.gz: OK
./POC-57-TP1_R2_001.fastq.gz: OK
./POC-57-TP2_R1_001.fastq.gz: OK
./POC-57-TP2_R2_001.fastq.gz: OK
./POC-57-TP3_R1_001.fastq.gz: OK
./POC-57-TP3_R2_001.fastq.gz: OK
./POC-57-TP4_R1_001.fastq.gz: OK
./POC-57-TP4_R2_001.fastq.gz: OK

4 FastQC/MultiQC on raw reads

# Load bash variables into memory
source .bashvars

# Make output directory if it doesn't exist
mkdir --parents "${raw_reads_dir}"

############ RUN FASTQC ############


# Create array of trimmed FastQs
raw_fastqs_array=(${raw_reads_dir}/${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
### NOTE: Do NOT quote raw_fastqc_list
${programs_array[fastqc]} \
--threads ${threads} \
--outdir ${raw_reads_dir} \
--quiet \
${raw_fastqc_list}

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

############ END FASTQC ############

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

${programs_array[multiqc]} ${raw_reads_dir} -o ${raw_reads_dir}

echo ""
echo "MultiQC on raw FastQs complete."
echo ""

############ END MULTIQC ############

echo "Removing FastQC zip files."
echo ""
rm ${raw_reads_dir}/*.zip
echo "FastQC zip files removed."
echo ""
Beginning FastQC on raw reads...

application/gzip
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FastQC on raw reads complete!

Beginning MultiQC on raw FastQC...


  /// MultiQC 🔍 | v1.14

|           multiqc | MultiQC Version v1.27 now available!
|           multiqc | Search path : /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/F-Ptua/data/rnaseq-raw-fastqs
|         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 312/312  
|            fastqc | Found 78 reports
|           multiqc | Compressing plot data
|           multiqc | Report      : ../data/rnaseq-raw-fastqs/multiqc_report.html
|           multiqc | Data        : ../data/rnaseq-raw-fastqs/multiqc_data
|           multiqc | MultiQC complete
|           multiqc | 1 flat-image plot used in the report due to large sample numbers
|           multiqc | To force interactive plots, use the '--interactive' flag. 
See the documentation.

MultiQC on raw FastQs complete.

Removing FastQC zip files.

FastQC zip files removed.
# Load bash variables into memory
source .bashvars

# View directory contents
ls -lh ${raw_reads_dir}
total 100G
drwxr-xr-x 2 sam sam  4.0K Feb 20 15:25 multiqc_data
-rw-r--r-- 1 sam sam  2.2M Feb 20 15:25 multiqc_report.html
-rw-r--r-- 1 sam sam  599K Feb 20 15:17 POC-201-TP1_R1_001_fastqc.html
-rw-r--r-- 1 sam sam  1.3G Oct  3 12:50 POC-201-TP1_R1_001.fastq.gz
-rw-r--r-- 1 sam sam    64 Feb 20 15:08 POC-201-TP1_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  604K Feb 20 15:18 POC-201-TP1_R2_001_fastqc.html
-rw-r--r-- 1 sam sam  1.3G Oct  3 12:52 POC-201-TP1_R2_001.fastq.gz
-rw-r--r-- 1 sam sam    64 Feb 20 15:08 POC-201-TP1_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  601K Feb 20 15:18 POC-201-TP2_R1_001_fastqc.html
-rw-r--r-- 1 sam sam  1.5G Oct  3 14:25 POC-201-TP2_R1_001.fastq.gz
-rw-r--r-- 1 sam sam    64 Feb 20 15:08 POC-201-TP2_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  603K Feb 20 15:19 POC-201-TP2_R2_001_fastqc.html
-rw-r--r-- 1 sam sam  1.5G Oct  3 14:27 POC-201-TP2_R2_001.fastq.gz
-rw-r--r-- 1 sam sam    64 Feb 20 15:08 POC-201-TP2_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  618K Feb 20 15:17 POC-201-TP3_R1_001_fastqc.html
-rw-r--r-- 1 sam sam 1004M Oct  3 11:43 POC-201-TP3_R1_001.fastq.gz
-rw-r--r-- 1 sam sam    64 Feb 20 15:08 POC-201-TP3_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  626K Feb 20 15:16 POC-201-TP3_R2_001_fastqc.html
-rw-r--r-- 1 sam sam 1023M Oct  3 11:44 POC-201-TP3_R2_001.fastq.gz
-rw-r--r-- 1 sam sam    64 Feb 20 15:08 POC-201-TP3_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  603K Feb 20 15:18 POC-219-TP1_R1_001_fastqc.html
-rw-r--r-- 1 sam sam  1.4G Oct  3 14:44 POC-219-TP1_R1_001.fastq.gz
-rw-r--r-- 1 sam sam    64 Feb 20 15:08 POC-219-TP1_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  608K Feb 20 15:18 POC-219-TP1_R2_001_fastqc.html
-rw-r--r-- 1 sam sam  1.4G Oct  3 14:45 POC-219-TP1_R2_001.fastq.gz
-rw-r--r-- 1 sam sam    64 Feb 20 15:08 POC-219-TP1_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  604K Feb 20 15:17 POC-219-TP2_R1_001_fastqc.html
-rw-r--r-- 1 sam sam  1.3G Oct  3 15:31 POC-219-TP2_R1_001.fastq.gz
-rw-r--r-- 1 sam sam    64 Feb 20 15:08 POC-219-TP2_R1_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  609K Feb 20 15:18 POC-219-TP2_R2_001_fastqc.html
-rw-r--r-- 1 sam sam  1.3G Oct  3 15:33 POC-219-TP2_R2_001.fastq.gz
-rw-r--r-- 1 sam sam    64 Feb 20 15:08 POC-219-TP2_R2_001.fastq.gz.md5
-rw-r--r-- 1 sam sam  616K Feb 20 15:18 POC-219-TP3_R1_001_fastqc.html
-rw-r--r-- 1 sam sam  1.3G Oct  3 09:57 POC-219-TP3_R1_001.fastq.gz
-rw-r--r-- 1 sam sam    64 Feb 20 15:08 POC-219-TP3_R1_001.fastq.gz.md5
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RESULTS

MultiQC report:

Screenshot of trimmed MultiQC per base sequence content plot showing

MultiQC screencap showing Sequence Content.

Screenshot of MultiQC Adapter Content.

MultiQC screencap showing Adapter Content.

References

Ewels, Philip, Måns Magnusson, Sverker Lundin, and Max Käller. 2016. “MultiQC: Summarize Analysis Results for Multiple Tools and Samples in a Single Report.” Bioinformatics 32 (19): 3047–48. https://doi.org/10.1093/bioinformatics/btw354.