Post date: Sep 07, 2018 10:0:19 PM
We decided (in response to reviewer comments) to also try to identify inversions from the comparative alignment between the green and brown morph genomes. Specifically from the maf file mualnTcrBrwGrnDec16.maf in /uufs/chpc.utah.edu/common/home/u6000989/data/timema/tcrDovetail/MugsyComp. This was created with
bash
source /uufs/chpc.utah.edu/common/home/u6000989/source/mugsy_x86-64-v1r2.3/mugsyenv.sh
cd /scratch/general/lustre/gompMugsy/
/uufs/chpc.utah.edu/common/home/u6000989/source/mugsy_x86-64-v1r2.3/mugsy --directory /scratch/general/lustre/gompMugsy --prefix mualnTcrBrwGrnDec16 /uufs/chpc.utah.edu/common/home/u6000989/data/timema/tcrDovetail/version3/timema_06Jun2016_RvNkF702.fasta /uufs/chpc.utah.edu/common/home/u6000989/data/timema/tcrDovetail/timema_green_denovo/timema_green_22Dec2016_ycYxT/timema_green_22Dec2016_ycYxT.fasta
mv ./* /uufs/chpc.utah.edu/common/home/u6000989/data/timema/tcrDovetail/MugsyComp/
Note that in this file, the brown morph always is shown as a + orientation. The green can be + or -, where - is different from the brown morph and I think can be interpreted (mostly) as evidence of an inversion. The exception would be if the whole green scaffold is reverse complemented such that + would mean inverted and - normal (going to dig into this a bit more).
I ran my script ExtractInversions.pl on this maf file. It prints an inversions_*txt file that gives the brown genome scaffold, start, end and length for each inversion.
UPDATE. Ok, this is an issue. I made another script, MeasureOrientationFreqs.pl, that determines for each pair of scaffolds the proportion of the alignment that is ++ vs +-. My expectation was that for most it would mostly be ++. This isn't exactly true (see orientation*txt). About 70% of scaffold pairs have ++ majority and overall about 70% is ++. 87.5% of scaffolds have ++ or +- > 90%. In other words, there usually is a dominant orientation, but it isn't always ++. I think this means I should define inverted or not based on what the dominant orientation is for a pair.