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Benchmarking Data Set for Peak Callers -------------------------------------- This data set is designed to benchmark peak caller. It includes an aritifical genome, simulated background and experiment reads of different qualities as well as the gold standard for the peak locations. If you use this data set for benchmarks please cite the Sierra Platinum paper. Description of the directory contents 1)genome: genome.fa - sequence of the artifical genome with 10 chromsomes (CHR1,...,CHR10) in fasta format. 2) benchmarkingLocation: goldstandard.bed - genomic position of all modified histones (each line corresponds to one histone) goldstandard_merged.bed - genomic position of the modifed domains (subsequent modified histone merged into one domain) goldstandard_broad.bed - genomic location of the modified domains when assuming broad peaks (subsequent domains not more than 400bp apart from each other are merged into one broad domain) 3) experimentsFastq and backgroundFastq: In the directories experimentsFastq and backgroundFastq, the simulated sequencing reads for all benchmarks are contained. In the table below, experiment and background files are matched and the benchmark characteristics are annotated. Noise signal indicated whether the reads are generated for the gold stardard signal or for a random signal. The basewise quality indicates whether the average quality of the bases (high, mid, low). The under-sequenced, over-sequenced, and normal sequencing depth are annotated in the column 'sequencing depth'. The enrichment of the experiment signal over the background signal is listed as low, normal, or high signal-2-noise. For each combination of conditions, at least two replicates are generated. experiment File background file noise signal basewise quality sequencing depth signal-2-noise ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- experimentsFastq/exp1.fastq.gz backgroundFastq/wce1.fastq.gz no high normal normal experimentsFastq/exp2.fastq.gz backgroundFastq/wce2.fastq.gz no high normal normal experimentsFastq/exp3.fastq.gz backgroundFastq/wce3.fastq.gz no high normal normal experimentsFastq/exp4.fastq.gz backgroundFastq/wce4.fastq.gz no high normal normal experimentsFastq/exp5.fastq.gz backgroundFastq/wce5.fastq.gz no high normal normal experimentsFastq/exp6.fastq.gz backgroundFastq/wce6.fastq.gz no high normal normal experimentsFastq/exp_high_0.01_2_1.fastq.gz backgroundFastq/wce_high_0.01_2_1.fastq.gz no high under low experimentsFastq/exp_high_0.01_2_2.fastq.gz backgroundFastq/wce_high_0.01_2_2.fastq.gz no high under low experimentsFastq/exp_high_0.01_4_1.fastq.gz backgroundFastq/wce_high_0.01_4_1.fastq.gz no high under normal experimentsFastq/exp_high_0.01_4_2.fastq.gz backgroundFastq/wce_high_0.01_4_2.fastq.gz no high under normal experimentsFastq/exp_high_0.01_5_1.fastq.gz backgroundFastq/wce_high_0.01_5_1.fastq.gz no high under high experimentsFastq/exp_high_0.01_5_2.fastq.gz backgroundFastq/wce_high_0.01_5_2.fastq.gz no high under high experimentsFastq/exp_high_0.1_2_1.fastq.gz backgroundFastq/wce_high_0.1_2_1.fastq.gz no high normal low experimentsFastq/exp_high_0.1_2_2.fastq.gz backgroundFastq/wce_high_0.1_2_2.fastq.gz no high normal low experimentsFastq/exp_high_0.1_4_1.fastq.gz backgroundFastq/wce_high_0.1_4_1.fastq.gz no high normal normal experimentsFastq/exp_high_0.1_4_2.fastq.gz backgroundFastq/wce_high_0.1_4_2.fastq.gz no high normal normal experimentsFastq/exp_high_0.1_5_1.fastq.gz backgroundFastq/wce_high_0.1_5_1.fastq.gz no high normal high experimentsFastq/exp_high_0.1_5_2.fastq.gz backgroundFastq/wce_high_0.1_5_2.fastq.gz no high normal high experimentsFastq/exp_high_0.4_2_1.fastq.gz backgroundFastq/wce_high_0.4_2_1.fastq.gz no high over low experimentsFastq/exp_high_0.4_2_2.fastq.gz backgroundFastq/wce_high_0.4_2_2.fastq.gz no high over low experimentsFastq/exp_high_0.4_4_1.fastq.gz backgroundFastq/wce_high_0.4_4_1.fastq.gz no high over normal experimentsFastq/exp_high_0.4_4_2.fastq.gz backgroundFastq/wce_high_0.4_4_2.fastq.gz no high over normal experimentsFastq/exp_high_0.4_5_1.fastq.gz backgroundFastq/wce_high_0.4_5_1.fastq.gz no high over high experimentsFastq/exp_high_0.4_5_2.fastq.gz backgroundFastq/wce_high_0.4_5_2.fastq.gz no high over high experimentsFastq/exp_mid_0.01_2_1.fastq.gz backgroundFastq/wce_mid_0.01_2_1.fastq.gz no mid under low experimentsFastq/exp_mid_0.01_2_2.fastq.gz backgroundFastq/wce_mid_0.01_2_2.fastq.gz no mid under low experimentsFastq/exp_mid_0.01_4_1.fastq.gz backgroundFastq/wce_mid_0.01_4_1.fastq.gz no mid under normal experimentsFastq/exp_mid_0.01_4_2.fastq.gz backgroundFastq/wce_mid_0.01_4_2.fastq.gz no mid under normal experimentsFastq/exp_mid_0.01_5_1.fastq.gz backgroundFastq/wce_mid_0.01_5_1.fastq.gz no mid under high experimentsFastq/exp_mid_0.01_5_2.fastq.gz backgroundFastq/wce_mid_0.01_5_2.fastq.gz no mid under high experimentsFastq/exp_mid_0.1_2_1.fastq.gz backgroundFastq/wce_mid_0.1_2_1.fastq.gz no mid normal low experimentsFastq/exp_mid_0.1_2_2.fastq.gz backgroundFastq/wce_mid_0.1_2_2.fastq.gz no mid normal low experimentsFastq/exp_mid_0.1_4_1.fastq.gz backgroundFastq/wce_mid_0.1_4_1.fastq.gz no mid normal normal experimentsFastq/exp_mid_0.1_4_2.fastq.gz backgroundFastq/wce_mid_0.1_4_2.fastq.gz no mid normal normal experimentsFastq/exp_mid_0.1_5_1.fastq.gz backgroundFastq/wce_mid_0.1_5_1.fastq.gz no mid normal high experimentsFastq/exp_mid_0.1_5_2.fastq.gz backgroundFastq/wce_mid_0.1_5_2.fastq.gz no mid normal high experimentsFastq/exp_mid_0.4_2_1.fastq.gz backgroundFastq/wce_mid_0.4_2_1.fastq.gz no mid over low experimentsFastq/exp_mid_0.4_2_2.fastq.gz backgroundFastq/wce_mid_0.4_2_2.fastq.gz no mid over low experimentsFastq/exp_mid_0.4_4_1.fastq.gz backgroundFastq/wce_mid_0.4_4_1.fastq.gz no mid over normal experimentsFastq/exp_mid_0.4_4_2.fastq.gz backgroundFastq/wce_mid_0.4_4_2.fastq.gz no mid over normal experimentsFastq/exp_mid_0.4_5_1.fastq.gz backgroundFastq/wce_mid_0.4_5_1.fastq.gz no mid over high experimentsFastq/exp_mid_0.4_5_2.fastq.gz backgroundFastq/wce_mid_0.4_5_2.fastq.gz no mid over high experimentsFastq/exp_low_0.01_2_1.fastq.gz backgroundFastq/wce_low_0.01_2_1.fastq.gz no low under low experimentsFastq/exp_low_0.01_2_2.fastq.gz backgroundFastq/wce_low_0.01_2_2.fastq.gz no low under low experimentsFastq/exp_low_0.01_4_1.fastq.gz backgroundFastq/wce_low_0.01_4_1.fastq.gz no low under normal experimentsFastq/exp_low_0.01_4_2.fastq.gz backgroundFastq/wce_low_0.01_4_2.fastq.gz no low under normal experimentsFastq/exp_low_0.01_5_1.fastq.gz backgroundFastq/wce_low_0.01_5_1.fastq.gz no low under high experimentsFastq/exp_low_0.01_5_2.fastq.gz backgroundFastq/wce_low_0.01_5_2.fastq.gz no low under high experimentsFastq/exp_low_0.1_2_1.fastq.gz backgroundFastq/wce_low_0.1_2_1.fastq.gz no low normal low experimentsFastq/exp_low_0.1_2_2.fastq.gz backgroundFastq/wce_low_0.1_2_2.fastq.gz no low normal low experimentsFastq/exp_low_0.1_4_1.fastq.gz backgroundFastq/wce_low_0.1_4_1.fastq.gz no low normal normal experimentsFastq/exp_low_0.1_4_2.fastq.gz backgroundFastq/wce_low_0.1_4_2.fastq.gz no low normal normal experimentsFastq/exp_low_0.1_5_1.fastq.gz backgroundFastq/wce_low_0.1_5_1.fastq.gz no low normal high experimentsFastq/exp_low_0.1_5_2.fastq.gz backgroundFastq/wce_low_0.1_5_2.fastq.gz no low normal high experimentsFastq/exp_low_0.4_2_1.fastq.gz backgroundFastq/wce_low_0.4_2_1.fastq.gz no low over low experimentsFastq/exp_low_0.4_2_2.fastq.gz backgroundFastq/wce_low_0.4_2_2.fastq.gz no low over low experimentsFastq/exp_low_0.4_4_1.fastq.gz backgroundFastq/wce_low_0.4_4_1.fastq.gz no low over normal experimentsFastq/exp_low_0.4_4_2.fastq.gz backgroundFastq/wce_low_0.4_4_2.fastq.gz no low over normal experimentsFastq/exp_low_0.4_5_1.fastq.gz backgroundFastq/wce_low_0.4_5_1.fastq.gz no low over high experimentsFastq/exp_low_0.4_5_2.fastq.gz backgroundFastq/wce_low_0.4_5_2.fastq.gz no low over high experimentsFastq/exp_noise1.fastq.gz backgroundFastq/wce_noise1.fastq.gz yes high normal normal experimentsFastq/exp_noise2.fastq.gz backgroundFastq/wce_noise2.fastq.gz yes high normal normal experimentsFastq/exp_noise3.fastq.gz backgroundFastq/wce_noise3.fastq.gz yes high normal normal
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