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
miRDeep2analysis to markdown and HTML.
20231113
-Coral E5 (GitHub repo):
miRDeep2analysis finally completed after 72hrs (!).Started teasing out some of the results from the MiRDeep2 analysis.
20231109
-
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.
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- 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.
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.
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.