added parameters

experiments/test_experiment/README.md

@@ -5,7 +5,7 @@ We will use the following parameters for all simulations:
 1. 600 reference genomes, genes from 500 will be present in ref db, genes from the
 rest 100 will not be present in the ref db.
 1. 1M reads for each simulation
-1. 1000 genes for each simulation
+1. 10000 genes for each simulation
 1. 150bp read length
 1. No simulation errors
 

scripts/workflow.sh

@@ -22,6 +22,7 @@ kSize=7  # decreasing this increases sensitivity at cost of FP's
 refScale=10  # the higher this number, the faster things run, the smaller the database, at the cost of less sensitivity
 queryScale=1  # likely will want to keep this at one (no down-sampling of the query)
 thresholdBP=100  # this has the largest impact on FNs and FPs: setting it higher filters out more false positives, at the cost of more false negatives
+
 # download genomes
 echo "./get_reference_genomes.py -n $numGenomes -s $dataDir  -u"
 #./get_reference_genomes.py -n $numGenomes -s $dataDir  -u