Sam’s Notebook: Transcriptome Assembly – Geoduck Tissue-specific Assembly Gonad HiSeq and NovaSeq Data on Mox

I previously assembled and annotated P.generosa gonad transcriptome (20190318) using just our HiSeq data from our Illumina collaboration. This was a an oversight, as I didn’t realize that we also had NovaSeq RNAseq data. So, I’ve initiated another de novo assembly using Trinity incorporating both sets of data.

NovaSeq data had been previously trimmed.

Trimming of the HiSeq data was performed via Trinity, using the --trimmomatic option.

SBATCH script (GitHub):

  #!/bin/bash ## Job Name #SBATCH --job-name=trin_gonad ## Allocation Definition #SBATCH --account=coenv #SBATCH --partition=coenv ## Resources ## Nodes #SBATCH --nodes=1 ## Walltime (days-hours:minutes:seconds format) #SBATCH --time=30-00:00:00 ## 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 --workdir=/gscratch/scrubbed/samwhite/outputs/20190409_trinity_pgen_gonad_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 >> system_path.log echo "" >> system_path.log echo "System PATH for $SLURM_JOB_ID" >> system_path.log echo "" >> system_path.log printf "%0.s-" {1..10} >> system_path.log echo ${PATH} | tr : \\n >> system_path.log # User-defined variables reads_dir=/gscratch/scrubbed/samwhite/data/P_generosa/RNAseq/gonad threads=28 assembly_stats=assembly_stats.txt # Paths to programs trinity_dir="/gscratch/srlab/programs/Trinity-v2.8.3" samtools="/gscratch/srlab/programs/samtools-1.9/samtools" ## Inititalize arrays R1_array=() R2_array=() # Variables for R1/R2 lists R1_list="" R2_list="" # Create array of fastq R1 files R1_array=(${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 ${trinity_dir}/Trinity \ --trimmomatic \ --seqType fq \ --max_memory 120G \ --CPU ${threads} \ --left \ ${R1_list} \ --right \ ${R2_list} # Assembly stats ${trinity_dir}/util/TrinityStats.pl trinity_out_dir/Trinity.fasta \ > ${assembly_stats} # Create gene map files ${trinity_dir}/util/support_scripts/get_Trinity_gene_to_trans_map.pl \ trinity_out_dir/Trinity.fasta \ > trinity_out_dir/Trinity.fasta.gene_trans_map # Create FastA index ${samtools} faidx \ trinity_out_dir/Trinity.fasta