Daily Bits - November 2022

20221121

• Lab meeting

• Short day due to early out for Audrey’s school.

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20221118

• Short day due to early out for Audrey’s school.

• Meeting with Linda Rhodes

  • Re-ran Jupyter Notebook using her original Silva files, but set to 99% clustering.

  • Reviewed using Conda environments.

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20221117

• Pub-a-thon

• Dealt with some power outages in the morning.

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2022116

• Went in to lab.

  • Showed Arianna around, got her keys, etc.

  • Updated/restarted Raven.

  • Worked on generating gene methylation coefficients of variation.

    • Struggled with converting data frame to matrix (required for rowcvs()).

    • RStudio Server locked up for a significant period of time.

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20221115

• Worked heavily on CEABIGR CoV gene methylation.

• Worked heavily on CEABIGR diffs in max transcripts and mean gene methylation.

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20221114

• Lab Meeting.

  • Discussed Ch.7 of The Disordered Cosmos

• C.virginica gene expression/DNA methylation meeting.

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20221110

• Sort of giving up on the Circos exploration - plots of the data we have don’t really fit into the Circos mode of data analysis (Circos is generally set up to examine spatial relationships of genome features).

• Started trying to make dot plots of the differences between the maximum number of transcripts per gene.

20221108

• Messed around a tiny bit with gettting max transcript count differences formatted for Circos.

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20221107

• Lab meeting.

• C.virginica oyster gene expression meeting (i.e. CEABIGR)

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20221104

• Meeting with Linda Rhodes to discuss 16s results

• Science Hour

• Oyster meeting with Lotterhos group to dicuss CEABIGR data.

• Power outage for a couple of hours…

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20221103

• Worked a bit on looking at Laura’s M.magister MBD-BSseq FastQC data (GitHub Issue).

• Pub-a-thon.

• Worked a bit on looking into Linda Rhodes 16s pipeline to see if we can figure out how to speed up the vsearch step. Nothing definitive found yet.

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20221102

• Finished updating the Ballgown Rmd script for CEABIGR repo.

  • Updated corresponding REAMDE(s) with file descriptions for output(s) from Rmd.

• Possibly fixed owl/nightingales Synology Glacier backup. Existing Glacier backup was consistently failing immediately with unhelpful log message.

  • Created new backup task.

    • US West (Oregon).

    • New key/private key for Amazon AWS Glacier vault.

    • Task is running and has backed up ~265GB so far (out of 13.03TB). Will monitor progress over the next couple of weeks/months.

• Worked on CEABIGR manuscript.

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20221101

• Worked on CEABIGR manuscript

• Transferred and updated Ballgown Rmd script to CEABIGR repo.