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Benchmark data sets: miRNA

Data sources

  • miRNA: http://www.mirbase.org/
  • noise: 2 sources of noise:
    • viral genomes of:
      • Acute_Bee_paralysis_virus_isolated_Poland_1
      • Chikungunya_virus_strain_TSI-GSD-218-VR1
      • European_bat_lyssavirus_2_isolate_RV1333
      • Lac_victoria_Marburg_virus_Angola_2005_Strain_Ang1386
      • Potato_virus_Y
      • tomato_Ringspot_Virus
    • encode:
      • hg18_dna range=chr5:131284314-132284313 5'pad=0 3'pad=0 revComp=FALSE strand=? repeatMasking=none

Sets

About the data:

  • size of R (nb of references): 6
  • references length (min/avg/max): 70 / 77.6 / 87
  • size of T: 50
  • size of T2: 150
  • size of F (viral): 288
  • size of F2 (viral): 1122
  • size of F (encode): 300
  • size of F2 (encode): 1123

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 miRNA
cd miRNA
unzip ../brasero_miRNA.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 ../braseroAnalyzer_1.0.jar results_viral
java -jar ../braseroAnalyzer_1.0.jar results_encode
inkscape -z -A results_viral/all_snspRoc.pdf results_viral/all_snspRoc.svg
acroread results_viral/all_snspRoc.pdf
inkscape -z -A results_encode/all_snspRoc.pdf results_encode/all_snspRoc.svg
acroread results_encode/all_snspRoc.pdf
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Page last modified on December 09, 2010, at 03:23 PM EST