University of Pennsylvania, Institute for Translational Medicine and Therapeutics
University of Pennsylvania, Department of Genetics

Script

• Naive Read Proportioning (NRP) Script
  • This is the script used as a naive baseline method, however it performed nearly as well as the production methods on realistic data.

True counts tables

• Idealized Data
  • Hip1_3
  • Hip2_3
  • Hip4_3
  • Liv1_3
  • Liv3_3
  • Liv5_3
• Realistic Data
  • Summary count table for all samples

Fastq Files

• Idealized data:
  • Hip1_3 forward
  • Hip1_3 reverse
  • Hip2_3 forward
  • Hip2_3 reverse
  • Hip4_3 forward
  • Hip4_3 reverse
  • Liv1_3 forward
  • Liv1_3 reverse
  • Liv3_3 forward
  • Liv3_3 reverse
  • Liv5_3 forward
  • Liv5_3 reverse
• Realistic data
  • Hip1_4 forward
  • Hip1_4 reverse
  • Hip2_4 forward
  • Hip2_4 reverse
  • Hip3_4 forward
  • Hip3_4 reverse
  • Hip4_4 forward
  • Hip4_4 reverse
  • Hip5_4 forward
  • Hip5_4 reverse
  • Hip6_4 forward
  • Hip6_4 reverse
  • Liv1_4 forward
  • Liv1_4 reverse
  • Liv2_4 forward
  • Liv2_4 reverse
  • Liv3_4 forward
  • Liv3_4 reverse
  • Liv4_4 forward
  • Liv4_4 reverse
  • Liv5_4 forward
  • Liv5_4 reverse
  • Liv6_4 forward
  • Liv6_4 reverse

CIG Files (matching reads to trancripts)

• Idealized data:
  • Hip1_3
  • Hip2_3
  • Hip4_3
  • Liv1_3
  • Liv3_3
  • Liv5_3
• Realistic data
  • Hip1_4
  • Hip2_4
  • Hip3_4
  • Hip4_4
  • Hip5_4
  • Hip6_4
  • Liv1_4
  • Liv2_4
  • Liv3_4
  • Liv4_4
  • Liv5_4
  • Liv6_4

Dictionary

• Dictionary that matches BEERS gene ids to Ensembl gene and transcript ids