[HELICONIUS] Notes on the Heliconius genome call

[Stephen Richards]

Hi everyone, 

Here are my notes fro the heliconius genome call.

People (some were also lurking whose names I missed):
Adrianna, Bob, fringy, Kim, Steve, Jamie, John D. Marcus (congrats on the baby!) Owen.

1. Owen gave a general summary:
 - fairly good progress
 - mapping of races looks good - giving useful information
 - a fair bit of microsynteny, but longer rearrangements in comparisons to the silk worm
 - collecting embryos to redo RNAseq if necessary
- need a plan to get moving on the annotation - which was the main thrust of the call.

2. Jamie gave a detailed description of his work so far.
 - he has a handle on the RNAseq thing, -although the data we supplied form Baylor is weird- but hard to quantify how weird due to lack of time, 
 - main problem is too many reads are mapping to multiple places in the genome, and the rRNA component is too high.
 - does have Augustus predictions from Mario Stanke, which were specially trained
 - does have the repeat libraries and screening sorted out
 - has ran tophat and cufflinks
 - starting in earnest on Maker (after some distractions) next Monday - expects a solid month and he will have Maker predictions.
 - was a short discussion about other gene proteins sets to put in for similarity evidence. Jamie is thinking about some protein data bases, and fringy suggested a few different genomes - which now I think about it would be fly, moth, beetle, bee, human, and head louse as comprehensive enough. The issue Jamie brought up is some of these are ab-initio models, and so it can be a bit of a house of cards, but hopefully the RNAseq data will help with that.

3. Bob talked about having the gmod set up but with little in it, 
 - it was decided that James in Bobs lab, should be in contact with Jamie to start with the Augustus predictions, the cufflinks output, and also add tracks for tblastn of other genomes protein sets to get started as evidence tracks to put in the browser. Also then they can use these to practice and ensure they will be ready immediately when the maker outputs are available. 
 - There was also discussion about the trade offs between annotating manually now vs later, and the need to have accurate gene models before phylogenetic work. It was decided that any manual annotations done now will have to be entered into the Apollo system that is being set up later to ensure they do not get lost, so if you have started on some annotation that can't wait please keep notes to enable this later.

4. Bob and Owen both talked about the need for a manual annotation meeting, and there was discussion of where and when.
 - The consensus was either Durham or Irvine, with Bob preferring Durham (NSCENT?), as they are set up for this kind of thing.
 - Owen will ask about NSCENT - as when they are available will affect this decision.
 - Owen will also send around possible times when they are available.
 - In general people were thinking May - although at the Baylor end Steve would like to avoid Biology of Genomes 

5. Owen reported that Erato sequence is available on the UCI server, although it has yet to be aligned to the melpomene genome.

6.  John said that the RadMapping is progressing

7. We forgot to talk about Chris's genome plots

8. I forgot to set up the next call.
Unless anyone objects I propose 11am US central time April 20th. Europe will be on Summer time then, 
so it will be back to 5pm in the UK.

Cheers, 

fringy