Shelly’s Notebook: Fri. Sept 21, 2018

My goals for today

  1. Review geoduck literature and grant
  2. Continue brainstorming ideas for october experiment
  3. Complete Bismark analysis
  4. Update on protein stuff from Kaitlyn @kaitlynrm

    #### Oyster proteomics: larvae in two different rearing temperatures
    -experiment: 15 days of rearing; one group (silo 3) at 23C and one (silo 9) at 29C
    -questions to address:
    1. Does 23C proteome differ from 29C proteome over time?
    2. Do the two 23C proteomes differ over time (silo 2 vs. silo 3)
    -need to determine which proteins between the two groups are different (e.g. show different abundance trends over time)
    -Try ACSA Ref for ASCA ; Ref for ASCA in metabolomics time series
    -Try Random Forest (can refer to its use in MetaboAnalyst; MetaboAnalystR) Random Forest Methods in metabolomics

Shelly’s Notebook: Thur. Sept 20, 2018

Met Steven and Katherine at Pt. Whitney

Toured facility and got pictures of OA experimental setup
Brainstormed some ideas for potential Geoduck broodstock experiments to start next month:
-seawater flowthough system needs to be set up
-have 6 boxes: 2 pH conditions x 3 replicates; 3 pH conditions x 2 replicates
-Things to think about:
-Ecological vs. aquacultural implications: Geoduck normally live in sand, boxes won’t have sand.
-Biology to explore:
1. Gonad development
2. Gametogenesis
3. Respirometry
4. lethal subsampling vs. hemolymph sampling (see Emma’s paper)
5. Metabolomics
-West Coast Metabolomics Core?
-UW mass spec core?
6. Epigenetics

Shelly’s Notebook: Wed. Sept 19, 2018

Progress on first Bismark analysis:

-Found a way to do my analysis/write files to the server but keep my Jupyter notebook in my github desktop folder see Jupyter notebook
-still working on code for generating Bismark summary files

### Miscelaneous progress:
-touched base with Katherine about Point Whitney tomorrow
-meeting with Kaitlyn about protein stuff (Got moved to Friday 9/21) -got a monitor, mouse, and keyboard from Mike in SAFS!
-got my personal info on the lab’s website

Shelly’s Notebook: My First Post

This is my first lab notebook post using GitHub’s markdown.

My goals today are to:

  1. Get my first lab notebook post out
  2. Start on my first task to familiarize with the lab’s general DNA methylation analysis pipeline for PE bisulfite sequencing data
  3. Try to find a monitor and keyboard from the surplus room in SAFS

This is an example of how to include images in posts and of how much I love shellfish an image alt text

Let’s see how this goes!

End-of-day Update:

  1. Post worked!
  2. Progress on first task:
    • Got server credentials and was able to mount servers to access data
    • Set up jupyter notebook. Found this tutorial helpful. Still need to work on how to sync with GitHub so large data files and analyses can be saved on the server.
    • Was able to download Bismark and get it to run locally on a subset of the data (10K reads). See details below. I did not do further analysis because I wanted to get the jupyter notebook fully set up and run the analysis on the server before getting too deep. -will continue to work on jupyter notebook setup and analysis tomorrow
  3. Went down to SAFS to ask Laurie about the surplus room, but she was in a meeting. Will try tomorrow

####################RUNNING BISMARK LOCALLY##################################### ##needed to install bowtie2 locally conda install -c bioconda bowtie2 ##needed to install samtools locally conda install -c bioconda samtools ##install bismark conda install -c bioconda bismark ##download genome locally curl https://ift.tt/2xirsAr > Cvirginica_v300.fa

##bismark genome preparation bismark_genome_preparation –path_to_bowtie /Users/Shelly/anaconda3/bin/ –verbose /Users/Shelly/Desktop/personal/Career/StevenRobetsLab/GENOMES/Cvirginica/v300 ###output from command => see below

#running bismark bismark -u 10000 –non_directional –score_min L,0,-0.6 –genome /Users/Shelly/Desktop/personal/Career/StevenRobetsLab/GENOMES/Cvirginica/v300/ -1 /Volumes/web/seashell/bu-serine-wd/18-04-07/R1.fastq.gz -2 /Volumes/web/seashell/bu-serine-wd/18-04-07/R2.fastq.gz

###############output from bismark alignment#######################

Path to Bowtie 2 specified as: bowtie2

Bowtie seems to be working fine (tested command ‘bowtie2 –version’ [2.3.4])

Output format is BAM (default)

Alignments will be written out in BAM format. Samtools found here: ‘/Users/Shelly/anaconda3/bin/samtools’

Reference genome folder provided is /Users/Shelly/Desktop/personal/Career/StevenRobetsLab/GENOMES/Cvirginica/v300/ (absolute path is ‘/Users/Shelly/Desktop/personal/Career/StevenRobetsLab/GENOMES/Cvirginica/v300/)’

FastQ format assumed (by default)

Processing sequences up to read no. 10000 from the input file

Input files to be analysed (in current folder ‘/Users/Shelly/Desktop/personal/Career/StevenRobetsLab/data_analysis/Cvirg_Apr2018/Bismark_attempt1’):

/Volumes/web/seashell/bu-serine-wd/18-04-07/zr2096_1_s1_R1.fastq.gz

/Volumes/web/seashell/bu-serine-wd/18-04-07/zr2096_1_s1_R2.fastq.gz

Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!)

Setting parallelization to single-threaded (default)

Current working directory is: /Users/Shelly/Desktop/personal/Career/StevenRobetsLab/data_analysis/Cvirg_Apr2018/Bismark_attempt1

Now reading in and storing sequence information of the genome specified in: /Users/Shelly/Desktop/personal/Career/StevenRobetsLab/GENOMES/Cvirginica/v300/

chr NC_035780.1 (65668440 bp)

chr NC_035781.1 (61752955 bp)

chr NC_035782.1 (77061148 bp)

chr NC_035783.1 (59691872 bp)

chr NC_035784.1 (98698416 bp)

chr NC_035785.1 (51258098 bp)

chr NC_035786.1 (57830854 bp)

chr NC_035787.1 (75944018 bp)

chr NC_035788.1 (104168038 bp)

chr NC_035789.1 (32650045 bp)

chr NC_007175.2 (17244 bp)

Single-core mode: setting pid to 1

Paired-end alignments will be performed