Genome size estimation of skimming data (RESPECT)

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 ..