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@adamthrash: Can you look into chromosomer transfer to copy the annotations over to the new assemblies? The new assemblies are in analysis/assemble/chromosomer.

Chromosomer

https://github.com/gtamazian/chromosomer

Install

# Code written from memory (not run)
swsetup python
virtualenv chromosomer
source chromosomer/bin/activate
pip install chromosomer
deactivate

Setup

export PYTHONPATH=`pwd`/chromosomer/lib/python2.7/
PATH=$PATH:`pwd`/chromosomer/bin/

• Genome size estimation via kmers

date repeat clusters using method in https://github.com/Wendellab/KokiaKirkii/blob/master/analysis/clustering/te_dating.sh

modify to include species test for each cluster

We need to revamp the phylogeny of the D-genome, minimally for ancestral state reconstructions. Introgression among members of the D-genome and with other cottons complicate this, mostly for G. gossypioides. I cannot use the cpDNA phylogeny because it has chloroplast introgression from G. raimondii.

Nuclear phylogeny of the D-genome:
RaxML + Astral: does astral actually give branch lengths (required for ancestral state reconstruction)?

MrBayes+TICR: can I get this pipeline to work....??

@maa146 , could you upload or send me updated tables/stats for the assemblies? I need number of reads (raw and trimmed); fold coverage; assembly stats; annotation stats; busco stats; etc for each accession.

Submit the chloroplasts to ncbi.

ancestral states will be constructed for overall genome size and for "clusters of interest"

Meeting with Tracy Heath next week to discuss this. Copy number is a discrete trait, so using the same reconstruction method as genome size will not work. I'm thinking RevBayes with a chromosome number evolution-like model

We need to run gatk to call indels for the resequencing. It should be done with the bam files where the reads were mapped against the D-genome, and it should include all Ds (that have respectable coverage) plus F1.

Adam, Tony said that he will catch you up tomorrow and ask you to do this. I'm toying with the idea of using GitHub projects/issues to keep track of tasks; hence, the open issue.