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