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Benchmark data sets: tRNA

Data sources

  • tRNA:
  • noise: 4 sources of noise:
    • viral genomes of:
      • AF486073.2
      • DQ447655
      • EF452494.1
      • NC_001616.1
      • NC_003839.2
    • encode:
      • hg18_dna range=chr5:131284314-132284313 5'pad=0 3'pad=0 revComp=FALSE strand=? repeatMasking=none
    • GenRGenS: random structures that look like tRNA
    • GenRGenS: random structures refolded

Sets

About the data:

  • size of R (nb of references): 6
  • references length (min/avg/max): 68 / 71.833 / 81
  • size of T: 139 * size of T2: 692
  • size of F (viral): 294 * size of F2 (viral): 1104
  • size of F (encode): 300 * size of F2 (encode): 1108
  • size of F (GenRGenS): - * size of F2 (GenRGenS): 600
  • size of F (GenRGenS refolded): 600
  • size of F2 (GenRGenS refolded): 2132

How to run the benchmarking engine on this benchmark

We assume all requirements are satisfied (see benchmarking tools, and that a file tools.xml is present in the current directory.

 
mkdir tRNA 
cd tRNA 
unzip ../brasero_tRNA.zip 
cp ../tools.xml . 
java -jar ../braseroComparator_1.0.jar -d results_viral references_set true_events_with_viral_noise_set tools.xml 
java -jar ../braseroComparator_1.0.jar -d results_encode references_set true_events_with_encode_noise_set tools.xml 
java -jar ../braseroComparator_1.0.jar -d results_genrgens references_set true_events_with_genrgens_generated_noise_set tools.xml 
java -jar ../braseroComparator_1.0.jar -d results_genrgens_refolded references_set true_events_with_genrgens_refolded_noise_set tools.xml 
for d in results_viral results_encode results_genrgens results_genrgens_refolded 
do  
   java -jar ../braseroAnalyzer_1.0.jar $d  
   inkscape -z -A $d/all_snspRoc.pdf $d/all_snspRoc.svg  
done 
acroread results_*/all_snspRoc.pdf 
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Page last modified on December 09, 2010, at 03:19 PM EST