Yaamini’s Notebook: April 2018 Goals

April showers = More writing hours

#FakeApril has begun, and it’s brought some rainy days! Time to curl up under my blanket with a cup of chai and get to writing.

March Goals Recap:

DNR:

  • I FINISHED THE DNR PAPER (well, sent a clean, full draft to Emma, Brent and Steven)
  • Haven’t finalized repository contents, supplemental information, or sent a draft to the other co-authors because writing a discussion took way longer than I anticipated (pretty sure my brain hurt for 3 days straight)

Manchester:

Virginica:

  • I did not set up my analysis pipeline 😦

Metaanalysis:

  • lol
  • I’m just going to go ahead and table this until 1) I submit my DNR paper, 2) I submit my Manchester paper, and 3) Pub-a-thon starts

Other:

  • Reading a paper every day doesn’t work for my ability to retain information. I’m more of a “read a fat stack of papers at all once” person. I did go through at least 30-40 papers this month while writing my DNR paper and preparing for my NSA talk!
  • Reading and attending NSA 2018 helped me come up with some ideas for next steps!

April Goals:

DNR:

  • Send paper to other co-authors for comments
  • Combine supplementary information and finalize paper repository
  • Submit paper for publication!

Manchester:

  • Channel my inner Mac and write an entire paper and submit it in one month

Virginica:

  • My C. virginica MBD-Seq data came in! My goal is to set-up the pipeline and begin analyses

Other:

  • Write down project ideas for my Ph.D since I now have an NSF GRFP
  • Develop our lab’s outreach activity for the SEAS Open House
  • Create a lesson plan for the #scicomm lesson I’m leading for the Outreach to Diverse Audiences in Aquatic and Fishery Sciences class I’m co-facilitating

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Sam’s Notebook:Gunzip – Trimmed Illumina HiSeq Genome Sequencing Data

0000-0002-2747-368X

In preparation to run SpareAssembler, I needed to gunzip the trimmed gzipped FASTQ files from 20140401.

Ran the following slurm script on our Mox node:

  #!/bin/bash ## Job Name #SBATCH --job-name=20180404_geoduck_gunzip ## Allocation Definition #SBATCH --account=srlab #SBATCH --partition=srlab ## Resources ## Nodes (We only get 1, so this is fixed) #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 --workdir=/gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck for i in /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/*.gz; do filename="${i##*/}" no_ext="${filename%%.*}" gunzip < "$i" > "$no_ext".fastq done  
Results:

This crashed shortly after initiating the run (~30mins later). Received following email notification:

SLURM Job_id=155940 Name=20180404_geoduck_gunzip Failed, Run time 00:30:40, NODE_FAIL

It did not generate a slurm output file. Will contact UW IT…

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Sam’s Notebook:TrimGalore!/FastQC/MultiQC – Illumina HiSeq Genome Sequencing Data Continued

0000-0002-2747-368X

The previous attempt at this was interrupted by a random glitch with our Mox HPC node.

I removed the last files processed by TrimGalore!, just in case they were incomplete. I updated the slurm script to process only the remaining files that had not been processed when the Mox glitch happened (including the files I deemed “incomplete”).

As in the initial run, I kept the option in TrimGalore! to automatically run FastQC on the trimmed output files.

TrimGalore! slurm script: 20180401_trim_galore_illumina_geoduck_hiseq_slurm.sh

MultiQC was run locally once the files were copied to Owl.

Results:

Job completed on 20180404.

Trimmed FASTQs: 20180328_trim_galore_illumina_hiseq_geoduck/

MD5 checksums: 20180328_trim_galore_illumina_hiseq_geoduck/checksums.md5

  • MD5 checksums were generated on Mox node and verified after copying to Owl.

Slurm output file: 20180401_trim_galore_illumina_geoduck_hiseq_slurm.sh

TrimGalore! output: 20180328_trim_galore_illumina_hiseq_geoduck/20180404_trimgalore_reports/

FastQC output: 20180328_trim_galore_illumina_hiseq_geoduck/20180328_fastqc_trimmed_hiseq_geoduck/

MultiQC output: 20180328_trim_galore_illumina_hiseq_geoduck/20180328_fastqc_trimmed_hiseq_geoduck/multiqc_data/

MultiQC HTML report: 20180328_trim_galore_illumina_hiseq_geoduck/20180328_fastqc_trimmed_hiseq_geoduck/multiqc_data/multiqc_report.html

//

Trimming completed and the FastQC results look much better than before.

Will proceed with full-blown assembly!

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Sam’s Notebook:Titrations – Yaamini’s Seawater Samples

0000-0002-2747-368X

All data is deposited in the following GitHub repo:

Sample sizes: ~50g

LabX Method:

Daily pH calibration data file:

Daily pH log file:

Titrant batch:

CRM Batch:

Daily CRM data file:

Sample data file(s):

See metadata file for sample info (including links to master samples sheets):

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Sam’s Notebook:Titrations – Yaamini’s Seawater Samples

0000-0002-2747-368X

All data is deposited in the following GitHub repo:

Sample sizes: ~50g

LabX Methods:

Daily pH calibration data file:

Daily pH log file:

Titrant batch:

CRM Batch:

Daily CRM data file:

Sample data file(s):

See metadata file for sample info (including links to master samples sheets):

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Grace’s Notebook: April 3, 2018, RNA Isolation continued

RNA Isolation

Today I isolated another batch of RNA! I totally missed the isopropanol in the flammables cabinet – quite embarrassing. However, it wasn’t listed in the MyChem inventory… but I did look at that bottle multiple times and it just didn’t register in my brain that it was what I was looking for. Isopropanol can also be called “2-propanol”, which was the label on the bottle I had been using thus far.

Anyway, so I was happy to continue with the RNA isolations today.

img

Qubit Results

Another successful day!

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Cummulative Qubit Results

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