We can tally the number of predicted misassembles. This will be evidence of errors in de novo assembly OR errors in reference genome.

If we the same region of reference tagged as a misassembly across more than one plant variety, we can ascertain that the do novo is likely correct and the reference is wrong!

Added RNA Spades short report to the google sheet.

link: https://docs.google.com/spreadsheets/d/1aQ1OTgE7Qiofr5Hn4W36JtvcUzHlhdS4FByZUj3E9ro/edit?usp=sharing

This short report is fantastic. And the results are going to be useful.
I am not sure the next steps. Need to think about this.

RNAQUAST has now been run on both Trinity and RNA-Spades.

Time to compare the 2 runs and see how they differ.

Here are the metrics that get measured:

SHORT SUMMARY REPORT

METRICS/TRANSCRIPTS

DATABASE METRICS
Genes
Avg. number of exons per isoform

BASIC TRANSCRIPTS METRICS
Transcripts
Transcripts > 500 bp
Transcripts > 1000 bp

ALIGNMENT METRICS
Aligned
Uniquely aligned
Multiply aligned
Unaligned

ALIGNMENT METRICS FOR NON-MISASSEMBLED TRANSCRIPTS
Avg. aligned fraction
Avg. alignment length
Avg. mismatches per transcript

ALIGNMENT METRICS FOR MISASSEMBLED (CHIMERIC) TRANSCRIPTS
Misassemblies

ASSEMBLY COMPLETENESS (SENSITIVITY)
Database coverage
Duplication ratio
50%-assembled genes
95%-assembled genes
50%-covered genes
95%-covered genes
50%-assembled isoforms
95%-assembled isoforms
50%-covered isoforms
95%-covered isoforms
Mean isoform coverage
Mean isoform assembly

ASSEMBLY SPECIFICITY
50%-matched
95%-matched
Unannotated
Mean fraction of transcript matched

Brandon, can you add the figures you generated to here?

RNA SPADES: https://drive.google.com/drive/folders/1Rc6HxmNSXXDPZyPifcrvcqCWzSOoYvql?usp=sharing
TRINITY: https://drive.google.com/drive/folders/1q8EXgtFcJhxlZxlx1varNqnVFEqXU-G4?usp=sharing

I created some google folders to store the images.

Graphs added to a google drive.

https://drive.google.com/drive/folders/1Rc6HxmNSXXDPZyPifcrvcqCWzSOoYvql?usp=drive_link

Next phase is to interpret these.
This is ready for closing.