Sam’s Notebook: FastQC – WGBS Sequencing Data from Genewiz Received 20190408

We received whole genome bisulfite sequencing (WGBS) data from Genewiz last week on 20190408, so ran FastQC on the files on my computer (swoose). FastQC results will be added to Nightingales Google Sheet.

Each set of FastQs were processed with a bash script. This file (ends with .sh) can be found in each corresponding output folder (see below).

Sam’s Notebook: Transcriptome Assembly – Geoduck Tissue-specific Assembly Larvae Day5 EPI99 with HiSeq and NovaSeq Data on Mox

I previously assembled and annotated P.generosa larval Day 5 transcriptome (20190318 – mislabeled as Juvenile Day 5 in my previous notebook entries) 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.

Ran a de novo assembly on our HiSeq and NovaSeq data from Hollie’s larval Day 5 EPI 99 sample. This was done for Christian to use in some long, non-coding RNA (lncRNA) analysis.

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_epi99 ## 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_EPI99_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 ${PATH} | tr : \\n >> system_path.log # User-defined variables reads_dir=/gscratch/scrubbed/samwhite/data/P_generosa/RNAseq/epi_115 threads=28 assembly_stats=assembly_stats.txt # Paths to programs trinity_dir="/gscratch/srlab/programs/Trinity-v2.8.3" samtools="/gscratch/srlab/programs/samtools-1.9/samtools" ## Inititalize arrays R1_array=() R2_array=() # Variables for R1/R2 lists R1_list="" R2_list="" # Create array of fastq R1 files R1_array=(${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 

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 

Sam’s Notebook: Transcriptome Assembly – Geoduck Tissue-specific Assembly Juvenile Ambient OA EPI124 with HiSeq and NovaSeq Data on Mox

Ran a de novo assembly on our HiSeq and NovaSeq data from Hollie’s juvenile EPI 124 sample “ambient OA”. This was done for Christian to use in some long, non-coding RNA (lncRNA) analysis.

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_epi124 ## 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_EPI124_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 ${PATH} | tr : \\n >> system_path.log # User-defined variables reads_dir=/gscratch/scrubbed/samwhite/data/P_generosa/RNAseq/epi_124 threads=28 assembly_stats=assembly_stats.txt # Paths to programs trinity_dir="/gscratch/srlab/programs/Trinity-v2.8.3" samtools="/gscratch/srlab/programs/samtools-1.9/samtools" ## Inititalize arrays R1_array=() R2_array=() # Variables for R1/R2 lists R1_list="" R2_list="" # Create array of fastq R1 files R1_array=(${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 

Sam’s Notebook: Transcriptome Assembly – Geoduck Tissue-specific Assembly Juvenile Ambient OA EPI123 with HiSeq Data on Mox

Ran a de novo assembly on our HiSeq data from Hollie’s juvenile EPI 123 sample “ambient OA”. This was done for Christian to use in some long, non-coding RNA (lncRNA) analysis.

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

SBATCH script (GitHub):

  #!/bin/bash ## Job Name #SBATCH --job-name=trin_epi123 ## 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_EPI123_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 ${PATH} | tr : \\n >> system_path.log # User-defined variables reads_dir=/gscratch/scrubbed/samwhite/data/P_generosa/RNAseq/epi_123 threads=28 assembly_stats=assembly_stats.txt # Paths to programs trinity_dir="/gscratch/srlab/programs/Trinity-v2.8.3" samtools="/gscratch/srlab/programs/samtools-1.9/samtools" ## Inititalize arrays R1_array=() R2_array=() # Variables for R1/R2 lists R1_list="" R2_list="" # Create array of fastq R1 files R1_array=(${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 

Sam’s Notebook: Transcriptome Assembly – Geoduck Tissue-specific Assembly Juvenile Super Low OA EPI116 with HiSeq and NovaSeq Data on Mox

Ran a de novo assembly on our HiSeq and NovaSeq data from Hollie’s juvenile EPI 116 sample “super low OA”. This was done for Christian to use in some long, non-coding RNA (lncRNA) analysis.

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_epi116 ## 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_EPI116_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 ${PATH} | tr : \\n >> system_path.log # User-defined variables reads_dir=/gscratch/scrubbed/samwhite/data/P_generosa/RNAseq/epi_116 threads=28 assembly_stats=assembly_stats.txt # Paths to programs trinity_dir="/gscratch/srlab/programs/Trinity-v2.8.3" samtools="/gscratch/srlab/programs/samtools-1.9/samtools" ## Inititalize arrays R1_array=() R2_array=() # Variables for R1/R2 lists R1_list="" R2_list="" # Create array of fastq R1 files R1_array=(${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