Finish run through of Ptuh lncRNA discovery pipeline with GFFcompare edits. Altered GTF formatting code. Confirmed final files do not have duplicates. Link to notebook post.
Summarize the projects and findings from FISH 460 lab experiments. Link to notebook post.
Set-up summer daily notebook post.
June 24
Annual review and summer planning meeting with Steven
Set-up hack-a-thon for this week
Figured out why 0 counts across all samples for given lncRNAs in deep-dive-expression matrices by altering FeatureCounts settings. Link to notebook post.
June 25
Hack-a-thon
Re-run FeatureCounts code for Ptuh lncRNAs to confirms setting changes will add counts to 0 count rows. Create lab notebook post and github issue response for this problem. Link to notebook post.
Fixed hack-a-thon conferencing
Set-up new Pearson’s correlation code for revised lncRNA count matrices
June 26
Hack-a-thon
Review of current status of first 2 chapter manuscripts and key areas for finishing rough drafts. Link to notebook post.
Check-in with Madeline and job/internship/grad school application tips
Setting up new Pearson’s correlation code for lncRNA-mRNA co-expression
June 30
Finish adapting PCC code from Kathleen and Jill to work on Raven for mRNA-lncRNA
Extend re-run code for Apul and Peve lncRNA ID and count matrix generation
July 1
PCC code adaptation notebook post
Travel day to CO
July 2 - 6
CO visit with family and roadtrip to Texas, mostly off