Sam’s Notebook: Transcriptome Assembly – Hematodinium with MEGAN6 Taxonomy-specific Reads with Trinity on Mox

Ran a de novo assembly using [the extracted reads classified under Alveolata from 20200122].(https://ift.tt/2RhkjuM) The assembly was performed with Trinity on Mox.

SBATCH script (GitHub):

#!/bin/bash ## Job Name #SBATCH --job-name=trinity_hemat ## Allocation Definition #SBATCH --account=srlab #SBATCH --partition=srlab ## Resources ## Nodes #SBATCH --nodes=1 ## Walltime (days-hours:minutes:seconds format) #SBATCH --time=10-00:00:00 ## 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/20200122_hemat_trinity_megan_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/srlab/sam/data/C_bairdi/RNAseq threads=27 assembly_stats=assembly_stats.txt timestamp=$(date +%Y%m%d) fasta_name="${timestamp}.hemat.megan.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=(${reads_dir}/*_R1.fq) # Create array of fastq R2 files R2_array=(${reads_dir}/*_R2.fq) # Create list of fastq files used in analysis ## Uses parameter substitution to strip leading path from filename for fastq in ${reads_dir}/*.fq do echo "${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 120G \ --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}