--- author: Sam White toc-title: Contents toc-depth: 5 toc-location: left layout: post title: FastQ Trimming and QC - C.virginica Larval BS-seq Data from Lotterhos Lab and Part of CEABIGR Project Using fastp on Mox date: '2022-08-29 07:04' tags: - BSseq - Lotterhos - CEABIGR - Crassostrea virginica - Eastern oyster - fastp - mox categories: - 2022 - Miscellaneous --- We had some old [_Crassostrea virginica_ (Eastern oyster)](https://en.wikipedia.org/wiki/Eastern_oyster) larval/zygote BS-seq data from the Lotterhos Lab that's part of the [CEABiGR Workshop/Project](https://github.com/sr320/ceabigr) (GitHub Repo) and Steven asked that I QC/trim it in [this GitHub Issue](https://github.com/RobertsLab/resources/issues/1517). The original data/experiment is described in this repo (NOTE: this might be a private repo...): - [epigeneticstoocean/2018OAExp_larvae](https://github.com/epigeneticstoocean/2018OAExp_larvae) Metadat for the files processed in this notebook: - [2018_L18_OAExp_Cvirginica_DNAm/blob/main/data/L18_larvae_meta.csv](https://github.com/epigeneticstoocean/2018_L18_OAExp_Cvirginica_DNAm/blob/main/data/L18_larvae_meta.csv) Some notes: - FastQs were concatenated prior to trimming, as each sample had been sequenced twice to get desired sequencing depth. - Noted when initially transferred data from Lotterhos Lab (via Alan Downey-Wall) - missing some second run FastQ files (these have not been ): - CF01-CM01-Zygote_R1_001.fastq.gz - CF08-CM04-Larvae_R2_001.fastq.gz - EF03-EM03-Zygote_R2_001.fastq.gz - Note from Alan Downey-Wall regarding sample naming: > The Sample.ID​ contains the mothersID-fathersID-stage (zygote or 4 day larvae) for each offspring pool. I trimmed with [`fastp`](https://github.com/OpenGene/fastp) and performed trimming QC summary using [`MultiQC`](https://multiqc.info/). The job was run on Mox. See [RESULTS section for lists of files processed](#results) SBATCH script (GitHub): - [20220826-cvir-larvae_zygote-BSseq-fastp_trimming.sh](https://github.com/RobertsLab/sams-notebook/blob/master/sbatch_scripts/20220826-cvir-larvae_zygote-BSseq-fastp_trimming.sh) ```bash #!/bin/bash ## Job Name #SBATCH --job-name=20220826-cvir-larvae_zygote-RNAseq-fastp_trimming ## Allocation Definition #SBATCH --account=coenv #SBATCH --partition=coenv ## Resources ## Nodes #SBATCH --nodes=1 ## Walltime (days-hours:minutes:seconds format) #SBATCH --time=10-00:00:00 ## Memory per node #SBATCH --mem=200G ##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/20220826-cvir-larvae_zygote-BSseq-fastp_trimming ### Lotterhos C.virginica larvae and gonad BSseq trimming using fastp, and MultiQC. ### Expects input FastQ files to be in format: EF03-EM04-Larvae_R1_001.fastq.gz ################################################################################### # These variables need to be set by user # 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 ## Raw reads directory raw_reads_dir=/gscratch/scrubbed/samwhite/data/C_virginica/BSseq ## checksum files trimmed_checksums=trimmed-fastq-checksums.md5 raw_fastq_checksums=raw-fastq-checksums.md5 input_fastq_checksums=input-fastq-checksums.md5 # Paths to programs fastp=/gscratch/srlab/programs/fastp-0.20.0/fastp multiqc=/gscratch/srlab/programs/anaconda3/bin/multiqc ## Inititalize arrays fastq_array_R1=() fastq_array_R2=() R1_names_array=() R2_names_array=() # Programs associative array declare -A programs_array programs_array=( [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=$(date +%Y%m%d) # Concatenate FastQ files from 1st and 2nd runs # Do NOT quote fastq_pattern variable # Will rsync all first run FastQs to working directory first, # as there are missing second run FastQs; making concatenation process more complicated # than I want to deal with. for first_run_fastq in "${raw_reads_dir}"2018OALarvae_DNAm_discovery/${fastq_pattern} do echo "Generating checksums for raw input FastQs..." # Strip full path to just get filename. first_run_fastq_name="${first_run_fastq##*/}" # Determine MD5 checksum md5sum "${first_run_fastq}" | tee --append "${raw_fastq_checksums}" echo "" # Rsync FastQ echo "Rsyncing ${first_run_fastq} to working directory." rsync -aP "${first_run_fastq}" . echo "Finished rsyncing ${first_run_fastq}." echo "" # Process second run and concatenate with corresponding FastQ from first run # Do NOT quote fastq_pattern variable for second_run_fastq in "${raw_reads_dir}"2018OALarvae_DNAm_discovery/second_lane/${fastq_pattern} do # Strip full path to just get filename. second_run_fastq_name="${second_run_fastq##*/}" # Concatenate FastQs with same filenames if [[ "${first_run_fastq_name}" == "${second_run_fastq_name}" ]]; then echo "Concatenating ${first_run_fastq_name} with ${second_run_fastq} to ${first_run_fastq_name}" echo "" cat "${second_run_fastq}" >> "${first_run_fastq_name}" fi done echo "Generating checksums for concatenated FastQs..." md5sum "${first_run_fastq_name}" | tee --append "${input_fastq_checksums}" echo "" done # Generate MD5 checksums for second run of FastQs # Do NOT quote fastq_pattern variable for second_run_fastq in "${raw_reads_dir}"2018OALarvae_DNAm_discovery/${fastq_pattern} do echo "Generating checksums for second run raw input FastQs..." # Determine MD5 checksum md5sum "${second_run_fastq}" | tee --append "${raw_fastq_checksums}" echo "" done echo "" echo "FastQ concatenation complete." echo "" # 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+=(${fastq%%.*}) done # Run fastp on files # Adds JSON report output for downstream usage by MultiQC echo "Beginning fastp trimming." echo "" for index in "${!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 \ --thread ${threads} \ --html "${R1_sample_name}".fastp-trim."${timestamp}".report.html \ --json "${R1_sample_name}".fastp-trim."${timestamp}".report.json \ --out1 "${R1_sample_name}".fastp-trim."${timestamp}".fq.gz \ --out2 "${R2_sample_name}".fastp-trim."${timestamp}".fq.gz # Generate md5 checksums for newly trimmed files { md5sum "${R1_sample_name}".fastp-trim."${timestamp}".fq.gz md5sum "${R2_sample_name}".fastp-trim."${timestamp}".fq.gz } >> "${trimmed_checksums}" # 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 "fastp trimming complete." echo "" # Run MultiQC echo "Beginning MultiQC..." echo "" ${multiqc} . echo "" echo "MultiQC complete." echo "" #################################################################### # Capture program options if [[ "${#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 ``` --- # RESULTS Runtime was surprisingly long, ~13hrs: ![Screencap of Mox runtime for fastp trimming of C.virginica larval/zygote FastQs from inbox](https://github.com/RobertsLab/sams-notebook/blob/master/images/screencaps/20220826-cvir-larvae_zygote-BSseq-fastp_trimming-runtime.png?raw=true) Output folder: - [20220826-cvir-larvae_zygote-BSseq-fastp_trimming](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/) #### MultiQC Report (HTML - opens in web browser) - [20220826-cvir-larvae_zygote-BSseq-fastp_trimming/multiqc_report.html](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/multiqc_report.html) #### MD5 Checksum files (text) - [input-fastq-checksums.md5](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/input-fastq-checksums.md5) (128K) - [raw-fastq-checksums.md5](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/raw-fastq-checksums.md5) (128K) - [trimmed-fastq-checksums.md5](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/trimmed-fastq-checksums.md5) (128K) ### Trimmed FastQs - [CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz) (1.7G) - MD5: `12f8df2981cbd6a2721b9ab74a317823` - [CF01-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/CF01-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz) (1.8G) - MD5: `e380280e9081a2dd9d205ddbae411eb2` - [CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/CF01-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz) (6.8G) - MD5: `5683f4e247f65e2b89ad751d3015941e` - [CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/CF01-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz) (7.1G) - MD5: `b2ffa5a04395936522057632c16bbf5f` - [CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/CF02-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz) (11G) - MD5: `5d49bdeccf3137855a218bb12f8718bc` - [CF02-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/CF02-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz) (11G) - MD5: `12a19d7ab32821bfc3c56b3bb4960963` - [CF03-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/CF03-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz) (6.6G) - MD5: `eb0e3fa10019ff57efe03a1337cda541` - [CF03-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/CF03-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz) (6.7G) - MD5: `c54595a4dfbf19d3957395bae9b78dca` - [CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/CF03-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz) (6.4G) - MD5: `ca8abb9fda4d9d658bac1f9f703fca99` - [CF03-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/CF03-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz) (6.7G) - MD5: `6a3d24e35cd393ee7b90e9642c0e6211` - [CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/CF03-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz) (6.3G) - MD5: `d580dbf84db9d9ce1c46c30007ec0558` - [CF03-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/CF03-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz) (6.5G) - MD5: `dafeacd05ceae42b9ec10894344fd8d4` - [CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/CF04-CM04-Zygote_R1_001.fastp-trim.20220827.fq.gz) (6.8G) - MD5: `90aadd64eeee0f4acd035b1551a47c72` - [CF04-CM04-Zygote_R2_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/CF04-CM04-Zygote_R2_001.fastp-trim.20220827.fq.gz) (7.0G) - MD5: `04ece2ff54e39f7ba008454a120db956` - [CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz) (8.7G) - MD5: `c77a953bad8db1a01ff122b60447f60f` - [CF05-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/CF05-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz) (9.1G) - MD5: `4528d42e50cf70651214d1355ccbbd03` - [CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/CF05-CM05-Zygote_R1_001.fastp-trim.20220827.fq.gz) (7.5G) - MD5: `73effea12236ec02f1582073fca9487d` - [CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/CF05-CM05-Zygote_R2_001.fastp-trim.20220827.fq.gz) (7.7G) - MD5: `1b195a1fd57bdd13cbe6b888283e6264` - [CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/CF06-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz) (7.4G) - MD5: `a0e154b0e75d7c8913ea8ad4e5c3273d` - [CF06-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/CF06-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz) (7.6G) - MD5: `3590c352a6e49a20c69be83843b9cd22` - [CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/CF06-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz) (6.0G) - MD5: `9b5ee60b0cf6524d914a81e91ba8f17e` - [CF06-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/CF06-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz) (6.3G) - MD5: `72c58d48baff2f6dcc9f7268bf5d0ee1` - [CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/CF07-CM02-Zygote_R1_001.fastp-trim.20220827.fq.gz) (11G) - MD5: `ea473ce9c2f9f80f0eeccc34c8ca31eb` - [CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/CF07-CM02-Zygote_R2_001.fastp-trim.20220827.fq.gz) (12G) - MD5: `007053a4002b5f0efe06722d55394747` - [CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/CF08-CM03-Zygote_R1_001.fastp-trim.20220827.fq.gz) (7.5G) - MD5: `01a1cd682959d947c5db82550bb58f07` - [CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/CF08-CM03-Zygote_R2_001.fastp-trim.20220827.fq.gz) (7.7G) - MD5: `9dc2701ae4c65e61fe182060f392edb1` - [CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/CF08-CM04-Larvae_R1_001.fastp-trim.20220827.fq.gz) (3.1G) - MD5: `d95f81647f43127e4e2868d2108cda1a` - [CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/CF08-CM04-Larvae_R2_001.fastp-trim.20220827.fq.gz) (3.2G) - MD5: `14de052215e0b1c244dcfcd1ef83ba3b` - [CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/CF08-CM05-Larvae_R1_001.fastp-trim.20220827.fq.gz) (4.8G) - MD5: `3151e296f863a8c72647112014ed4323` - [CF08-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/CF08-CM05-Larvae_R2_001.fastp-trim.20220827.fq.gz) (4.9G) - MD5: `e24e23cd1f2544d9242099bfed9feb63` - [EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/EF01-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz) (6.4G) - MD5: `8d13f56dbc64996b68d46eb3d6718bc0` - [EF01-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/EF01-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz) (6.7G) - MD5: `d2e807722434cb3e1f809b62bfe94e47` - [EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/EF02-EM02-Zygote_R1_001.fastp-trim.20220827.fq.gz) (7.0G) - MD5: `ba3c32f669c8cf7f8cebeaa326e2c124` - [EF02-EM02-Zygote_R2_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/EF02-EM02-Zygote_R2_001.fastp-trim.20220827.fq.gz) (7.2G) - MD5: `04363a049d229e293f55a353d86a9b7e` - [EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/EF03-EM03-Zygote_R1_001.fastp-trim.20220827.fq.gz) (6.6G) - MD5: `f87c5bd5dc936e31b24be6a4641533f4` - [EF03-EM03-Zygote_R2_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/EF03-EM03-Zygote_R2_001.fastp-trim.20220827.fq.gz) (6.8G) - MD5: `d22e3b366f7925dcd7f6423959a692c2` - [EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/EF03-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz) (7.1G) - MD5: `b86786ef26d0c457bc7cd9132171c6e5` - [EF03-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/EF03-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz) (7.3G) - MD5: `9955ad6581deeec0ef7a2a4fd3dc3add` - [EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/EF03-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz) (7.4G) - MD5: `b97793f3c112f99e684007afea1d3793` - [EF03-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/EF03-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz) (8.0G) - MD5: `e1f15320454cec901ff55c859faea251` - [EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/EF04-EM04-Zygote_R1_001.fastp-trim.20220827.fq.gz) (7.5G) - MD5: `db6a2f540da624f1d5f6e6f115e9be37` - [EF04-EM04-Zygote_R2_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/EF04-EM04-Zygote_R2_001.fastp-trim.20220827.fq.gz) (7.8G) - MD5: `3392de88b79f5d7ed869a361b210b6c1` - [EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/EF04-EM05-Larvae_R1_001.fastp-trim.20220827.fq.gz) (7.8G) - MD5: `82e93ae37039e2d364fae8456e8402bc` - [EF04-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/EF04-EM05-Larvae_R2_001.fastp-trim.20220827.fq.gz) (8.2G) - MD5: `2a97684b1ce7766e0bc6defc6c658f00` - [EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/EF05-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz) (5.9G) - MD5: `553cae24e62a3d9d13a40932f4abf7cd` - [EF05-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/EF05-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz) (6.1G) - MD5: `8bc90d15d6ea3dbf7fc3a0230946d393` - [EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/EF05-EM05-Zygote_R1_001.fastp-trim.20220827.fq.gz) (6.4G) - MD5: `0e485302097e7418cbb3e0da51c816d8` - [EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/EF05-EM05-Zygote_R2_001.fastp-trim.20220827.fq.gz) (6.6G) - MD5: `cda27057c4035d802eea34df4a205951` - [EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/EF05-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz) (12G) - MD5: `d3b29de534520e21e919e081893b24ef` - [EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/EF05-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz) (13G) - MD5: `6b49a13d08da78ac926f756c4535fbb0` - [EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/EF06-EM01-Larvae_R1_001.fastp-trim.20220827.fq.gz) (7.9G) - MD5: `2d15a505990a48b867d680b69888ea6e` - [EF06-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/EF06-EM01-Larvae_R2_001.fastp-trim.20220827.fq.gz) (8.3G) - MD5: `9742ad2f80aa34dbd823d893832fc260` - [EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/EF06-EM02-Larvae_R1_001.fastp-trim.20220827.fq.gz) (6.1G) - MD5: `19a757707e3fed916a8543cafbba7da4` - [EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/EF06-EM02-Larvae_R2_001.fastp-trim.20220827.fq.gz) (6.4G) - MD5: `116ee8a54cfb88dd6f03ceee5d7678ed` - [EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/EF06-EM06-Larvae_R1_001.fastp-trim.20220827.fq.gz) (8.2G) - MD5: `cdd926c032dff99c4e1805085c6ba2dc` - [EF06-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/EF06-EM06-Larvae_R2_001.fastp-trim.20220827.fq.gz) (8.4G) - MD5: `e489f1dd1e96af1de0195574753488be` - [EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/EF07-EM01-Zygote_R1_001.fastp-trim.20220827.fq.gz) (13G) - MD5: `ce149c91743b5fec393fae482af3b299` - [EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/EF07-EM01-Zygote_R2_001.fastp-trim.20220827.fq.gz) (14G) - MD5: `4aa1860340ed7da0c8ffa79193c58403` - [EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/EF07-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz) (7.0G) - MD5: `17f9a6aaf6b9ad9bb8496668eb90d8f0` - [EF07-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/EF07-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz) (7.3G) - MD5: `f5c408282b5bd76ac723367e42c152a2` - [EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/EF08-EM03-Larvae_R1_001.fastp-trim.20220827.fq.gz) (8.2G) - MD5: `b351e650cae8b4b7157abcfdc5af1b1b` - [EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/EF08-EM03-Larvae_R2_001.fastp-trim.20220827.fq.gz) (8.5G) - MD5: `4ad43654c347859cebc1b4dab3abe2fa` - [EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/EF08-EM04-Larvae_R1_001.fastp-trim.20220827.fq.gz) (5.8G) - MD5: `1f0711648941a4427f0ad643a8eccbfa` - [EF08-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz](https://gannet.fish.washington.edu/Atumefaciens/20220826-cvir-larvae_zygote-BSseq-fastp_trimming/EF08-EM04-Larvae_R2_001.fastp-trim.20220827.fq.gz) (6.0G) - MD5: `f5bc8a42549642cda5a9294567933321`