Daily Bits - November 2023

20231130

• Lab meeting.

  • Finished plotting task from yesterday.

• CEABIGR (GitHub repo) meeting.

  • Identified definition of spurious transcription and how to calculate.

20231129

• ProCard reconciliation.

• Worked on task for tomorrow’s lab meeting.

• Meeting with Daniell. Made a couple of suggestsions for her to work on:

  • Develop/teach Apptainers (Singularity).

  • Develop BLAST/UniProt/GO annotation pipeline.

20231117

Coral E5 (GitHub repo)

• Finished adding numbers to presentation.

• E5 molecular meeting

  • Decided to re-evaluate trimming, due to lack of matches in R2 reads.

20231116

• Coral E5 (GitHub repo):

  • Continued P.evermanni sRNAseq analysis.

  • Work on presentation for tomorrow.

• CEABIGR (GitHub repo)

  • Discussed spurious transcription:

    • Decided to calculate exon expression regression (GitHub Issue)

• Helped Grace L. with a git/GitHub issue on Raven (committed files which were too big for GitHub).

20231115

• Coral E5 (GitHub repo):

  • Started P.evermanni sRNAseq analysis.

20231114

-Coral E5 (GitHub repo):

• Knitted miRDeep2 analysis to markdown and HTML.

20231113

-Coral E5 (GitHub repo):

• miRDeep2 analysis finally completed after 72hrs (!).

• Started teasing out some of the results from the MiRDeep2 analysis.

20231109

• DuMOAR

  • Ran DIAMOND BLASTx to use for Trinotate.

  • Ran Trinotate.

20231108

• Coral E5

  • Dealt with the trials and tribulations of getting miRDeep2 to run. There are a lot of “hidden” file formatting requirements which aren’t documented until a job fails. Even then, the error messages don’t provide any advice. However, finally got it running!

• Read Ch. 1 of “Race After Technology: The New Jim Code” by Ruha Benjamin for DEI bookclub discussion at tomorrow’s lab meeting.

20231107

• Coral E5

  • Ran NCBI BLASTn on A.pulcha sRNAseq.

• DuMOAR

  • Began transcriptome annotation (GitHub) issue with TransDecoder.

20231106

• ProCard reconciliation.

• Scan/upload packing slips for purchases to Workday.

• Coral E5

  • non-coding RNA meeting.

  • Begin miRNA BLASTn.

20231103

• Coral E5

  • Ran ShortStack on A.pulchra (uses A.millepora genome though, since no A.pulchra genome exists) sRNAseq reads to identify potential miRNAs.

    • 13-Apul-sRNAseq-ShortStack.Rmd

    • Wasted a lot time messing around/learning how to Knit documements in R Markdown.

20231102

• In lab.

• E5 lncRNA meeting.

• Lab meeting.

• CEABIGR meeting.

• Coral E5

  • Ran MirMachine to identify miRNAs in A.pulchra.

    • 12-Apul-sRNAseq-MirMachine.Rmd

20231101

• Read intro to “Race After Technology: Abolisitionist for the new Jim Code”.

• Coral E5

  • Ran miRTrace on A.pulcrha sRNAseq data to identify potential taxonomic origins of miRNAs.

    • 09-Apul-sRNAseq-miRTrace.Rmd