Latest updates

Goal: Manuscript draft complete.

More manual review was done to check differences between Araport11 proteins and draft TAIR12 proteins.

Final Apollo manual review stats (as of today)

Total genes reviewed: 4775 (607 more than last time)

GFF file status

• NOR2 and NOR4 annotations complete, GFF file in TAIR hands
• tandem repeat annotations complete, GFF file in TAIR hands
• 5srDNA/rRNA annotations complete, GFF file in TAIR hands
• lncRNA annotations complete, GFF file in TAIR hands
• TE annotations almost complete - final comparison of v12 vs. v11 annotations
• protein annotations almost complete - reviewing v11 AGI code carryover

Writing status (drafts present in shared Google Drive)

• assembly figure
• centromere figures
• NCBI prediction text and table
• protein coding manual review text, tables, figures
• ITR annotation and figures
• NOR2/4 figures

Freeze on manual edits in Apollo. Final Apollo manual review stats (as of today)

Total genes reviewed: 4168

Apollo manual review stats (as of today)

Apollo manual review stats (as of today)

Apollo manual review stats (as of today)

Apollo manual review stats (as of today)

Goal: Manuscript writing begins in earnest. 

Done: Google Drive for shared documents created.

Goals: All review, quality control, nomenclature resolution, rule-creation for annotation retention, coordinate updates for V12 should be completed by this date.

Final GFF2 data files from external annotation groups to TAIR.

Files expected: TEs, 5sRNAs, NOR2/NOR4, lncRNAs, TRASH pipeline results

Apollo manual review stats (as of today)

Apollo manual review stats (as of today)

Status check conference call

Most of the review, quality control, nomenclature resolution, rule-creation for annotation retention, coordinate updates for V12 should be completed by this date.

PAG 2024 Arabidopsis Informatics session 12:50 - 13:00 Pacific time (some slide presentations available here)

DEADLINE: sample GFF3 data files from external annotation groups to TAIR

Summary of other annotation-related activities and groups:

1. Transposable element reannotation (in progress)
   
   1. Alex Bousios (University of Sussex)
   2. Shujun Ou (Ohio State University)
   3. Zhigui Bao (Max Planck Tübingen)
2. integration of NOR2 and NOR4 into Col-CC (in progress)
   
   1. Craig Pikaard, Ramya Enganti, Dalen Fultz, Anastasia McKinlay (Indiana University)
   2. Korbinian Schneeberger, Xiao Dong, Raul Wijfjes (MPIPZ, Uni München)
3. rDNA reannotation (in progress)
   
   1. Craig Pikaard, Ramya Enganti, Dalen Fultz, Anastasia McKinlay (Indiana University)
   2. Ian Henderson, Piotr Wlodzimierz (University of Cambridge)
4. Tandem repeat reannotation (complete)
   
   1. Ian Henderson, Piotr Wlodzimierz (University of Cambridge)
5. lncRNA reannotation (in progress)
   
   1. Andrew Nelson, Caylyn Railey, Kyle Palos (Cornell University)
   2. Michael Schon (Wageningen University & Research)
   3. Thomas Blein (Centre national de la recherche scientifique, CNRS)
   4. Aleksandra Kornienko (Gregor Mendel Institute)
   5. Selene Fernandez Valverde (UNSW Sydney)

NEW TRACK:

RNAseq combined and recapped, coverage view - an even more reduced combined coverage view of ALL the 62 RNAseq tracks that resulted from sequential rounds of capping and merging instead of individual capping and then final merging (the scale bars will be different and more lowly expressed RNAseq reads will be more visible

NEW TRACKS:

1. RNAseq combined, coverage view - combined coverage view of ALL the 62 RNAseq tracks, partially filtered to remove alignments with extra long introns and with excessive coverage in certain regions capped to 200.
   
2. RNAseq capped and merged, reads - individual reads of all files that were not able to be filtered but were individually capped at 200 and then merged.
3. RNAseq filtered capped and merged, reads - individual reads of all files that were individually filtered, then capped at 200, and then merged.
   

Plant Biology 2023 in Savannah, GA: Plant Bioinformatics Resources for FAIR Agricultural Data Discovery and Reuse workshop (10:30 am - 12:30 pm)

Update on the reannotation effort included in the TAIR presentation

1. over 300 genes have been started, about 70 are done
2. 4 office hours held (Wednesdays by Slack)
3. discussions going on in Slack
   1. what to do with insertion of mt sequence in chr2 - annotate genes or not?
   2. should we have a scoring system for genes?
   3. new track suggestions
      1. PFAM domains  - community suggested, created, and loaded
      2. PANTHER families - community suggested, created, and loaded
   4. track metadata table available in Apollo Tips