# deandylationPaperFigureUpdates2
## April 15, 2024

After the latest denial from Genome Research, there are several new analyses we want to add.
Most require new data, but some of the below analyses (marked with an asterisk) can be done with the existing data.

1. Decapping comparison*
   - This will specifically require comparing the number of reads with their 5'ends near the TSS and those near the STOP codon.
   - Reviewer 2 of the recent pass suggested this analysis specifically for the role of *smg-5* in decapping.
   - I am going to attempt this analysis in `decappingQuantification.ipynb`.
2. Figure clarity*
   - One of the main issues that reviewer 2 had was the clarity of the figures.
     We will need to try some adjustments to see if we can make them clearer.
3. *smg-7* knockout:
    - New library and replicates produced at 25°C.
    - This will attempt to address several reviewers points regarding the *smg-5* side of our analyses
      lacking the direct connection to deadenylation that *smg-7* provides.