Post date: Dec 30, 2016 4:4:34 AM
The green vs. dark morph comparative alignment is in mualnTcrBrwGrnDec16.maf in /uufs/chpc.utah.edu/common/home/u6000989/data/timema/tcrDovetail/MugsyComp/. Following the suggestion from the Mugsy folks I used gmaj.jar to visualize the alignment (it takes the maf file as an argument). At least on my laptop, loading the whole file doesn't work. I used the script getLg8maf2.pl to get just the LG8 alignments. This generated lg8_mualnTcrBrwGrnDec16.maf, which can be loaded in gmaj.jar as follows:
java -Xmx14G -jar PATH/gmaj.jar lg8_mualnTcrBrwGrnDec16.maf
I explored patterns of alignments for 128 and 702.1. We still don't have a single green scaffold that fully spans the likely inversion breakpoints for either, orientations appear to flip at the boundary when considering different scaffolds, and green scaffolds right at the boundary look like a mess of mini-inversions. I have a lot more to do, but this suggests an inversion strongly. I say this in part because the orientation of scaffolds from the Hi-Res assembly from Dovetail appears to contain information (this was an actual estimate). See 'Conitg orienting' in this paper.