SHARPR (Systematic High-resolution Activation and Repression Profiling with Reporter-tiling)

SHARPR is software for analyzing Massively Parallel Reporter Assay tiling designs allowing mapping at high resolution activating and repressive nucleotides across thousands of regulatory regions.
  • Interactive browser of all tiled regions from Ernst et al 2016
  • SHARPR software (v1.0.2; version log)
  • SHARPR manual
  • Quick instructions on running SHARPR on example data:
    1. Install Java 1.6 or later if not already installed.
    2. Unzip the file SHARPR.zip.
    3. To run SHARPR on the sample data to infer base level predictions directly from count data type from the SHARPR directory:
    java -mx2000M -jar SHARPR.jar ExecuteAll EXAMPLE/HepG2_ScaleUpDesign1_minP_mRNA_Rep1.counts,EXAMPLE/HepG2_ScaleUpDesign1_minP_mRNA_Rep2.counts EXAMPLE/ScaleUpDesign1_minP_Plasmid.counts,EXAMPLE/ScaleUpDesign1_minP_Plasmid.counts 3 145 5 31 EXAMPLE/basepredictions_HepG2_ScaleUpDesign1_minP.txt
  • SHARPR is described in:
    Ernst J#, Melnikov A, Zhang X, Wang L, Rogov P, Mikkelsen T, Kellis M#.
    Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions.
    Nature Biotechnology, 34:1180-1190, 2016.
  • Files specific to the Ernst et al manuscript:
    • Pilot (LargeStep) Raw Counts and Design Files
    • Pilot (LargeStep) Normalized Data Tables
    • Scale-up (SmallStep) Raw Counts and Design Files
    • Scale-up (SmallStep) Sharpr-MPRA Regulatory Activity Scores: HepG2 and K562
    • Scale-up (SmallStep) Browser Files (BigWig - hg19): HepG2 combinedP, K562 combinedP, HepG2 minP, K562 minP, HepG2 SV40P, K562 SV40P
    • Scale-up (SmallStep) Image Files: HepG2 Images, K562 Images
    • Data in GEO

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  • SHARPR source code on GitHub. SHARPR makes use of The Apache Commons Mathematics Library (v3.3).
  • Funding for SHARPR provided by NIH grants R01ES024995, U01HG007912 and U01MH105578 (J.E.), R01HG006785 (T.S.M.), R01GM113708, U01HG007610, R01HG004037, U54HG006991 and U41HG007000 (M.K.), an NSF CAREER Award #1254200, and an Alfred P. Sloan Fellowship (J.E.).