Daily Archives: January 3

genefish 23:11 on January 3  

Grace’s Notebook: January 2019 Goals

2015 Oysterseed DIA

  • Finish data analysis
  • Edit paper with new methods, etc.

Crab Project

RNA extractions

  • Re-run bioanalyzer on samples from Qiagen RNeasy Kit extraction
  • Extract RNA from 3 or 4 samples (Day 26) using new Trizol LS Reagent (add to bioanalyzer chip with the re-run samples)
  • Test out kit on geoduck hemolymph samples

Assembled transcriptome

  • BLAST with nt taxonomy database and get Order, Class, etc.

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genefish 22:23 on January 3  

Sam’s Notebook: Metagenome Assembly – P.generosa Water Sample Trimmed HiSeqX Data Using Megahit on Mox

Attempting an assembly of our geoduck metagenomics HiSeqX data using Megahit (v.1.1.4) on a Mox node.

Assembly was run using default settings.

Assembly coverage was assessed using the following BBmap (v.38.34) scripts:

  • bbwrap.sh (alignments)
  • pileup.sh (coverage)

SBATCH script is linked here and pasted in full below:

  #!/bin/bash ## Job Name #SBATCH --job-name=megahit ## Allocation Definition #SBATCH --account=srlab #SBATCH --partition=srlab ## Resources ## Nodes #SBATCH --nodes=1 ## Walltime (days-hours:minutes:seconds format) #SBATCH --time=5-00:00:00 ## 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 --workdir=/gscratch/scrubbed/samwhite/outputs/20190102_metagenomics_geo_megahit # Load Python Mox module for Python module availability module load intel-python3_2017 # Load Open MPI module for parallel, multi-node processing module load icc_19-ompi_3.1.2 # SegFault fix? export THREADS_DAEMON_MODEL=1 # 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 # variables fastq_dir=/gscratch/srlab/sam/data/metagenomics/P_generosa megahit=/gscratch/srlab/programs/megahit_v1.1.4_LINUX_CPUONLY_x86_64-bin/megahit bbmap_dir=/gscratch/srlab/programs/bbmap_38.34 ## Inititalize arrays fastq_array_R1=() fastq_array_R2=() # Create array of fastq R1 files for fastq in ${fastq_dir}/*R1*.gz; do fastq_array_R1+=(${fastq}) done # Create array of fastq R2 files for fastq in ${fastq_dir}/*R2*.gz; do fastq_array_R2+=(${fastq}) done # Create comma-separated list of input files R1_fastq_list=$(IFS=,; echo "${fastq_array_R1[*]}") R2_fastq_list=$(IFS=,; echo "${fastq_array_R2[*]}") # Run Megahit using paired-end reads ${megahit} \ -1 ${R1_fastq_list} \ -2 ${R2_fastq_list} \ --num-cpu-threads 28 # Determine coverage ## Align reads with BBmap BBwrap ${bbmap_dir}/bbwrap.sh \ ref=megahit_out/final.contigs.fa \ in1=${R1_fastq_list} \ in2=${R2_fastq_list} \ out=aln.sam.gz ## Output contig coverage ${bbmap_dir}/pileup.sh \ in=aln.sam.gz \ out=coverage.txt
genefish 21:47 on January 3  

Yaamini’s Notebook: January 2019 Goals

fun

I slipped up and didn’t write December 2018 goals, but I have some shiny new goals for the first month of 2019!

November Goals Recap:

DNR:

  • Resubmitted my paper to MEPS! The latest version can be found on bioRXiv here. This was primarily done in December and it was my only goal before the quarter ended.

Virginica:

Gigas Broodstock:

  • Did not solidify which kit to use for sample preparation (yet)

Other:

  • Ran my second committee meeting! The committee is on board with me bypassing Winter 2019
  • Outlined my PhD proposal
  • Looked up bypass application requirements

January Goals

Virginica:

  • Find intersections betwen output from methylKit unite and genome feature files
  • Proportion test for DML/DMR location against unite output
  • See if SNP data or mapping efficiency contributes to poor PCA clustering
  • Identify some form of gene enrichment or functional description
  • Update methods and results

Gigas Broodstock:

  • Identify which kit to use for DNA sequencing preparation
  • Send samples for sequencing
  • Determine if RNA can be isolated

Bypass:

  • Finish draft Ph.D proposal
  • Update CV
  • Write bypass statement
  • Send bypass application to committee for approval
  • Submit bypass application

Other:

  • Apply for Husky100
  • Work on NSF GROW application
  • Look into FHL TA application

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