Post date: Sep 26, 2016 1:46:51 AM
We now have Dovetail genomes of green and brown morphs:
Green morph = /uufs/chpc.utah.edu/common/home/u6000989/data/timema/tcrDovetail/timema_green_02Sep2016_avKmb/timema_green_02Sep2016_avKmb.fasta
Dark (brown) morph = /uufs/chpc.utah.edu/common/home/u6000989/data/timema/tcrDovetail/version3/map_timema_06Jun2016_RvNkF702.fasta
The dark morph genome version I am using (1.3) includes linkage map information and is post splitting up scaffold 702. The green morph genome is unaltered relative to what we received from dovetail. Note that the old mugsy comparison between Dovetail 1.2 (or 2) and the original T. cristinae genome is now in /uufs/chpc.utah.edu/common/home/u6000989/data/timema/tcrDovetail/MugsyComp/dovetail1 (details here). The current one (dark vs. green) will eventually be in the dovetail3 sub-directory. Once again, I am using Mugsy for the analysis. Here is the script:
#!/bin/sh
#SBATCH --time=240:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=30
#SBATCH --account=gompert-kp
#SBATCH --partition=gompert-kp
#SBATCH --job-name=mugsy
#SBATCH --mail-type=FAIL
#SBATCH --mail-user=zach.gompert@usu.edu
echo ------------------------------------------------------
echo ------------------------------------------------------
echo SLURM: job identifier is $SLURM_JOBID
echo SLURM: job name is $SLURM_JOB_NAME
echo ------------------------------------------------------
bash
source /uufs/chpc.utah.edu/common/home/u6000989/source/mugsy_x86-64-v1r2.3/mugsyenv.sh
cd /uufs/chpc.utah.edu/common/home/u6000989/data/timema/tcrDovetail/MugsyComp
/uufs/chpc.utah.edu/common/home/u6000989/source/mugsy_x86-64-v1r2.3/mugsy --directory /uufs/chpc.utah.edu/common/home/u6000989/data/timema/tcrDovetail/MugsyComp/ --prefix mualnTcrBrwGrn /uufs/chpc.utah.edu/common/home/u6000989/data/timema/tcrDovetail/version3/map_timema_06Jun2016_RvNkF702.fasta /uufs/chpc.utah.edu/common/home/u6000989/data/timema/tcrDovetail/timema_green_02Sep2016_avKmb/timema_green_02Sep2016_avKmb.fasta