2. Repeat Spectra and better coverage estimates

We will now use RESPECT to compute the repeat structure of the genomes.

Running RESPECT

Prepare input

Make sure you are under the skmer-tutorial directory.

mkdir respect 
cd respect
mkdir inputs
cd inputs
## link to both skims and genomes here
ln -s ../../skims/nonhybrids/Saccharomyces_*fq ../../skmer-tutorial/nonhybrids/*fna .
cd ..

Now run the method:

### There is some ugliness having to do with licenses gurobi. We cannot just run respect. I will discuss during the tutorial. 
### /cluster/projects/nn9458k/oh
_know/teachers/smirarab/respect/gurobi912/linux64/bin/grbgetkey
### export GRB_LICENSE_FILE=`pwd`/gurobi.lic
respect -d inputs/ -N 100

This will take a minute or two.

Look at the summary of results and note the high level of accuracy comparing to genomes

### Examine genome length estimates
column -t estimated-parameters.txt|sort -k1

### And examine repeat spectra
cat estimated-spectra.txt |sort -k1|column -t
cd ..