Shelly’s Notebook: Thur. Dec. 19, Geoduck Brood Conditioning

Broodstock Experimental Setup

New algae feeding system

Matt set up a new algae feeing system!

  • all parts are listed below under the heading “Equipment received”
  • This is an image of the tank empty uc?export=view&id=15HXsbDojN97A0jxBvWhjLv9VDUducBfT
  • This is an image of the tank with algae being pumped in. The algae flows in by the float valve and is then pumped straight up through the flow meter. Excess algae (not going through the flow meter) gets overflowed back into the tank uc?export=view&id=1gy5i828fz2ryOlOXf9o8DBXY-XRNI-I1
  • The next two images show where the algae goes after it passes the flow meter, up and over into the manifold which feeds the totes uc?export=view&id=1hVcD_8v-dowquTg52s2aNZrZB1BJylvo uc?export=view&id=1kaB-Hh5LKCZ0z_rSwDnOh6LXs_dId2y8

Distributing Broodstock into treatment tanks

  • There were a total of ~120 broodstock that came in on 12/11/19 from Port Gamble. And there were 16 that came in on 10/17/19 (not sure where these came from; these will be used for commercial spawning)
  • Matt and I split out the broodstock randomly into the 4 experimental tanks:
    • B1 (pH7.2)
    • B2 (amb)
    • B4 (amb)
    • B5 (pH7.2)
    • we added 23 healthy looking animals/tank
  • Remaining 12/11/19 animals (~20) were put back in tank B6 to be used in commercial spawning

B1: uc?export=view&id=1XIgjyuVWah3fc4aAUIwgVnAb_qMB2AA7 uc?export=view&id=1yD3Wh4J7fvVZKrAnp9END0-F7SWlyYVP

B2: uc?export=view&id=1be7_Rtq4e0IJrCRmmcMtZ8rVyP0v9_Lf

B4: uc?export=view&id=1_bq1RqRNDIaXS_3ph2EkQtAMqIOl_WsX

B5: uc?export=view&id=1MPiWBTXWTaexwEkaKztty4wfPaloaKIY

B6: uc?export=view&id=1v5XFR9RorU9JQECOpO9jozz5pY0CvU78 uc?export=view&id=1tvXv2PHcKe0pbeSquOju9qzFG7ZH137t

B3 (silos with juveniles from Fall exp): uc?export=view&id=14nDzP-rc3geUYqZt0VoghPczLH_oIjx2

Water chem

FFAR meeting

Equipment received

next steps:

  • check Apex probe calibration
  • run water chem samples from 10/3/2019 and 10/18/2019
  • label broodstock with shellfish tags
  • take hemolymph samples from broodstock?
  • screen, clean and count juveniles in silos from Fall experiment

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Sam’s Notebook: Transcriptome Assembly – C.bairdi Trimmed RNAseq Using Trinity on Mox

Earlier today, I trimmed our existing C.bairdi RNAseq data, as part of producing generating a transcriptome (per this GitHub issue). After trimming, I performed a de novo assembly using Trinity (v2.9.0) with the stranded library option (--SS_lib_type RF) on Mox.

SBATCH script (GitHub):

#!/bin/bash ## Job Name #SBATCH --job-name=trin_cbai ## Allocation Definition #SBATCH --account=srlab #SBATCH --partition=srlab ## Resources ## Nodes #SBATCH --nodes=1 ## Walltime (days-hours:minutes:seconds format) #SBATCH --time=30-00:00:00 ## Memory per node #SBATCH --mem=500G ##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/20191218_cbai_trinity_RNAseq # Exit script if a command fails set -e # Load Python Mox module for Python module availability module load intel-python3_2017 # 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 # User-defined variables reads_dir=/gscratch/scrubbed/samwhite/outputs/20191218_cbai_fastp_RNAseq_trimming threads=27 assembly_stats=assembly_stats.txt timestamp=$(date +%Y%m%d) fasta_name="${timestamp}.C_bairdi.Trinity.fasta" # Paths to programs trinity_dir="/gscratch/srlab/programs/trinityrnaseq-v2.9.0" samtools="/gscratch/srlab/programs/samtools-1.10/samtools" ## Inititalize arrays R1_array=() R2_array=() # Variables for R1/R2 lists R1_list="" R2_list="" # Create array of fastq R1 files R1_array=(${reads_dir}/*_R1_*.gz) # Create array of fastq R2 files R2_array=(${reads_dir}/*_R2_*.gz) # Create list of fastq files used in analysis ## Uses parameter substitution to strip leading path from filename for fastq in ${reads_dir}/*.gz do echo "${fastq##*/}" >> fastq.list.txt done # Create comma-separated lists of FastQ reads R1_list=$(echo "${R1_array[@]}" | tr " " ",") R2_list=$(echo "${R2_array[@]}" | tr " " ",") # Run Trinity using "stranded" setting (--SS_lib_type) ${trinity_dir}/Trinity \ --seqType fq \ --max_memory 500G \ --CPU ${threads} \ --SS_lib_type RF \ --left "${R1_list}" \ --right "${R2_list}" # Rename generic assembly FastA mv trinity_out_dir/Trinity.fasta trinity_out_dir/${fasta_name} # Assembly stats ${trinity_dir}/util/TrinityStats.pl trinity_out_dir/${fasta_name} \ > ${assembly_stats} # Create gene map files ${trinity_dir}/util/support_scripts/get_Trinity_gene_to_trans_map.pl \ trinity_out_dir/${fasta_name} \ > trinity_out_dir/${fasta_name}.gene_trans_map # Create FastA index ${samtools} faidx \ trinity_out_dir/${fasta_name}