Daily Bits - August 2022

20220831

• Spent a lot of time messing around with Mixomics R package tutorials.

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20220830

• Messed around with Mixomics R package tutorials to see how we might use this for our CEABiGR analysis. Mostly just wanted to familiarize myself with how to format data to use in Mixomics package.

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20220829

• Took the day off.

• Created notebook for QC/trim CEABiGR larvae/zygote samples.

• Updated CEABiGR summary notebook with larval/zygote updates.

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20220826

• Took the day off.

• Worked on developing/running script to QC/trim CEABiGR larvae/zygote samples.

• Continued to help with Marta’s job for Stacks on Mox.

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20220825

• Continued to troubleshoot QIIME taxonomy assignments.

• Met with Linda Rhodes to review discuss QIIME issues.

• Pub-a-thon.

• Helped with Grace’s Trinity RNAseq assembly issues.

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20220824

• Took the day off.

• Updated all README files in project-lake-trout Repo

• Finished lean vs. siscowet Ballgown DEG/DET analysis in project-lake-trout (GitHub Repo).

• Continued to help with Marta’s job for Stacks on Mox.

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20220823

• All day troubleshooting Linda Rhodes QIIME2 stuff. Discovered sequences are already trimmed(?), but would like to look at the adapters.fa file which is referenced in her notebooks (she didn’t have this available at the beginning of this project, so I’m not sure what’s in that file).

• Reviewed Marta’s SBATCH file for Stacks and helped with a multitude of issues/errors.

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20220822

• Worked heavily on Linda Rhodes QIIME2 stuff. Getting odd results of most data having unassigned taxonomies; the rest assigned to eukaryotes…

• Located pre-formatted SILVA 138 files (finally!) (here - need to click on the red box to actually get to the links!), but got same results with taxonomic assignments…

• Lab meeting discussed Intro/Ch.1 of “The Disordered Cosmos”

• Reviewed Matt’s SBATCH script for Trinity assembly…

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20220819

• Took the day off.

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20220818

• Created S.namaycush genes-only BED file for use in Ballgown analysis.

• Started work on S.namaycush Ballgown analysis.

• Continued recreating SILVA databases (bayes classification step takes a LONG time - and there are two steps)

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20220817

• Recreated SILVA database(s) using more specific workflow. Hope to solve issue of no taxonomic assignments experienced yesterday. https://forum.qiime2.org/t/processing-filtering-and-evaluating-the-silva-database-and-other-reference-sequence-data-with-rescript/15494

• Established lake trout repo for Ballgown analysis: https://github.com/RobertsLab/project-lake-trout

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20220816

• Renewed formaldehyde training

• Renewed fire extinguisher training

• Worked through Linda Rhodes Jupyter Notebooks 2,3, & 4. Hit roadblock in 4 - need external file.

• Worked through Linda Rhodes Jupyter Notebook 8. End results of pipeline had no taxonomic assignments. Need to review process to determine what went wrong.

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20220815

• Lab meeting:

  • Decided on next book for book club: The Disordered Cosmos

  • Discussed Pub-a-thon

  • Had Dorothy show her mussel heat stress poster

• Internet outage at ~ 11AM … back on about 12PM

• Internet outage again at 13:15…14:15 it’s back on!

• Worked on getting through Linda’s Jupyter Notebooks 2 & 3.

• Helped with Grace’s Trinity RNAseq assembly issues.

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20220812

• Intalled newest version of Stacks on Mox (Stacks version - issue by Marta)

  1. wget https://catchenlab.life.illinois.edu/stacks/source/stacks-2.62.tar.gz
  2. tar -xzvf stacks-2.62.tar.gz
  3. cd stacks-2.62
  4. module load gcc/10.1.0: Had to load newer version of gcc because default version triggered an error when running make.
  5. make

• Science Hour:

  • Helped Grace get Trinity running on Mox as part of this issue: RNAseq workflow

• Helped Marta get Globus Connect Personal running for transferring data to/from Mox: Globus Connect Personal

20220811

• Worked a bit on Linda Rhodes 16s stuff.

• Did a lot of troubleshooting for lab people. See the following GitHub Issues:

  • RNAseq workflow - issue by Grace

  • Trinity error on Raven: no module name numpy - issue by Matt

  • Stacks version - issue by Marta

  • Install transrate on Raven - issue by Matt

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20220810

• Completed installation of transrate on Raven. Due to the fact that the hosting provider for TransRate binaries no longer exists, one cannot download the binaries needed to run it. So, instead, the process required the following:

  • Installation of RVM - a Ruby version manager. I followed the Ubuntu install instructions, which allows for a multi-user installation by default.

  • Added users the rvm group: sudo usermod -a -G rvm <username>

  • Activating a Ruby version: rvm use ruby-3.0.0

  • Install TransRate: gem install transrate

  • Install TransRate dependencies: transrate --install-deps all

  • Remove problematic library preventing salmon from working (solution courtesy of this GitHub repo Issue from unrelated software): rm /usr/share/rvm/gems/ruby-3.0.0/bin/librt.so.1

• Put script together for S.namaycush HISAT2 alignments and splice site identification.

• Internet died at 10:30… and came back ~13:30.

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20220809

• In lab today to address lab inspection deficiencies:

  • Waste collection request for most old chemicals (this was a lot of chemicals).

  • Printed new lab hazards sign and mounted outside of FTR 213.

  • Labeled acids and bases cabinets in FTR 213.

  • Ordered additional gas cylinder bracket for CO₂ cylinder in FTR 213.

  • Took liquid nitrogen training (now required training).

• Helped Dorothy get qPCR barplot exported from R to SVG to use in her poster.

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20220808

• Read Fresh Banana Leaves Ch. 8 for lab meeting.

• Lab meeting.

• Oyster gene expression meeting. Played with methylation percentages and grouping by data in R with Steven (he did most of the playing around in R).

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20220805

• Messed around with Dorothy’s data with Steven (he did most of the messing around) during Science Hour.

• Chatted with Zach regarding aligning data for identification of lncRNAs. Showed him the basic HiSat2 indexing/aligning options.

• Chatted with Zach regarding mussel primers from that FISH541 class. Told him to re-run class samples with primers - most failures during class likely due to inexperience with bench work.

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20220804

• In lab today.

• Re-ran ferritin qPCR with fresh primer stocks using Dorothy’s mussel cDNA.

• Annual UW lab safety inspection.

• Introduced Dorothy to R and R Studio on Raven.

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20220803

• Created notebook post for mussel RNA isolation and reverse transcription from 20220726

• Created notebook post for mussel qPCRs from 20220727

• Briefly review some of the qPCR data mentioned above.

• Resolved Sensaphone GitHub Issue

• Added generic reverse transcription protocol to lab handbook

• Reviewed lab safety documentation and personnel in preparation for lab safety inspection tomorrow.