Write paper:
Abstract
Introduction
Materials and Methods
Results
Discussion
Data availability, author contributions, funding, conflict of interest, acknowledgements
References
Assemble figures and legends

Additional information:

• Google Drive folder for initial paper (once we are closer to submission we will move it to Dropbox): https://drive.google.com/drive/folders/1reCWmYj7jnIYPjy9PHT1KtURPrCSUnyG?usp=sharing
• Special issue submission site for Frontiers: https://www.frontiersin.org/research-topics/24549/regulation-of-alternative-splicing-in-plant-stress-responses
• Example paper from Frontiers (where we may submit): https://www.frontiersin.org/articles/10.3389/fpls.2021.765003/full
• Author guidelines for Frontiers: https://www.frontiersin.org/about/author-guidelines

Generate files:
RNA-Seq: bam/bai, bedgraph scaled, junctions

• The NF-core pipeline most likely did not output bedgraph or junctions files (double-check on the cluster), so we will need to determine the best way to produce those files.
• There should be a read counts file in the salmon folder on the cluster. Need to pull it down so we can use it to rerun the differential expression analysis.

Many of the BS-Seq files are already in the quickload, but need to catalog those in the quickload and bitbucket:
BS-Seq: bam/bai, bed (DMR regions), bedgraph (methyldackel)

Upload new RNA-Seq files to quickload: http://lorainelab-quickload.scidas.org/saltyrice/
Confirm that all files are viewable in the rice O_sativa_japonica_Oct_2011 genome

The following tickets have been created:

IGBF-3091 Write Introduction
IGBF-3092 Write Materials and Methods
IGBF-3093 Write Discussion
IGBF-3094 Write Abstract
IGBF-3095 Assemble figures and legends
IGBF-3096 Assemble endnote library
IGBF-3097 Generate RNA-Seq bedgraph scaled files
IGBF-3098 Generate RNA-Seq junctions files
IGBF-3099 Analyze differential expression using RNA-Seq
IGBF-3100 Upload RNA-Seq files to Quickload
IGBF-3101 Catalog current results for BS-Seq data
IGBF-3102 Analyze differential splicing using RNA-Seq

Additional tasks will be necessary to better define the specific results required for the paper. IGBF-3045 has potential ideas for results.

Closing ticket.