Sam’s Notebook: FastQC-MultiQC – Additional C.gigas WGBS Sequencing Data from Genewiz Received 20190501

Earlier today, we received the additional G.gigas sequencing data from Genewiz. Wanted to run through FastQC again and get an updated report for each data set. Admittedly, it probably won’t look much different from the initial FastQC run on 20190415, due to the fact that the additional sequencing was simply appended to the previous data. Since FastQC examines a subset of the data in each file, I’d fully expect the FastQC report to look the same. However, we’ll have a greater number of sequences in each file. This should, in turn, increase the number of reads retained after quality trimming.

Ran FastQC, followed by MultiQC on my computer (swoose).

Used this bash script:

Grace’s Notebook: May Goals

Crab Project

  • Help with getting pooled samples submitted for library prep and sequencing to the NWGC
  • Think of what crab-related data that I have can be used for FISH 497 course

2015 Oytserseed Proteomic project

  • Finish paper solidly
  • Publish correct data and documents to PRIDE (proteomic data) and Panorama (SKyline doc)
  • Clean up paper repo

This project is so close to being totally done!!! It can and will be finished this month – submitted to BioRXiv and whatever else.

from Grace’s Lab Notebook

Yaamini’s Notebook: May 2019 Goals

Screen Shot 2019-04-28 at 1 18 16 PM


April Goals Recap:

i.e. me marveling at the ambition I had

Virginica Gonad Methylation:

  • Modified paper repo so analysis is easily reproducible
  • Refined my DML analysis and (almost) finished refning the general methylation analysis
  • Didnt’ get to DMR or gene-level analysis because I am still sorting out issues with the general methylation trend analysis

Virginica Sperm:

  • I was focusing on the gonad methylation paper so I haven’t thought about lab work


May Goals

i.e. me trying to set some realistic expectations for this month while also trying to achieve everything I didn’t do last week and making progress beyond that

Virginica Gonad Methylation:

  • Troubleshoot CpG counts and finalize general methylation trends by May 3
  • Preliminary description of genes with differentially methylated loci by May 5
  • Differentially methylated region analysis by May 7
  • Differentially methylated gene analysis by May 9
  • Discussion outline by May 9
  • Draft paper by May 12
  • Paper submission to bioRXiv by May 31

Gigas Gonad and Larvae Methylation:

  • Have MBD workflow meeting
  • Extract RNA
  • Process DNA for bisulfite sequencing
  • Send DNA and RNA for sequencing
  • Develop plan for processing larval samples

Virginica Sperm Methylation:

  • Identify samples for RNA-Seq
  • Extract RNA
  • Process DNA for bisulfite sequencing
  • Send DNA and RNA for sequencing


  • Identify a GSR
  • Schedule a committee meeting for summer

// Please enable JavaScript to view the comments powered by Disqus.

from the responsible grad student