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		  | Submission of ENCODE data |  
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		    We are looking forward to the submission of
                    ENCODE-related data, and are ready to help
                    throughout the process.  We recommend the
                    following steps: 
		     
			Choose an appropriate format 
			(BED, GFF,
		        GTF, MAF, or 
			WIG) for your data from the
		        descriptions below and create a 
		        file in that format. The submitted data file should be
			in plain-text (or compressed plain-text) format.Data coordinates should be based on the NCBI
			Build 35 assembly (May 2004, hg17). If necessary, 
			data in BED format from previous assemblies may be
			transformed to the Build 35 assembly with the UCSC
		        liftOver
		        tools.Test your file by loading it into the
                        browser as a 
			custom track.Generate a description page to accompany
			your data. The page should contain a brief
			description of the data, methods used
			to generate the data, the techniques used to
			verify the data, acknowledgements of the
			individuals or organizations involved in data
			collection and analysis, and any related literature 
			references (optional). Use the 
			HTML template 
			to organize and format your text.
		        When your data is displayed as you desire,
		        please 
		        contact us by email to encode@soe.ucsc.edu,
                        to initiate loading the tracks into the
		        database.  This makes the data available to
		        the rest of the ENCODE community and to the
		        public.
                        The status of your track at UCSC can be checked on the
                        
                        ENCODE data status page.
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		| Browser Extensible Data Format (BED) |  
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		        The BED format was defined for the efficient
		        storage and retrieval of genomic annotations.
		        It provides a flexible way to define the data
		        lines that are displayed in an annotation
		        track.  Please see the
			
		        BED format description on the 
		        
		        custom tracks page for more details.
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		  | General Feature Format (GFF) |  
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			GFF is used for data where there are a set of
			linked features, such as gene models that have
			introns, exons, promoters, and transcription
			start/end sites.  GFF lines have nine required
			fields that must be tab-separated. If the
			fields are separated by spaces instead of
			tabs, the track will not display correctly.
			Please see the
			
		        GFF description on the 
		        
		        custom tracks page for more details.
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		  | Gene Transfer Format (GTF) |  
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			GTF is a refinement of GFF that tightens the
			specification and allows arbitrary
			supplemental information for each gene.
			Please see the
			
		        GTF description on the 
		        
		        custom tracks page for more details.
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	   	  | Multiple Alignment Format (MAF) |  
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		        The multiple alignment format stores a series
		        of multiple alignments in a format that is
		        easy to parse and relatively easy to read.
		        This format stores multiple alignments at the
		        DNA level between entire genomes. 
			Please see the
			
		        MAF description help page 
			for more details.
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		        The wiggle (WIG) format allows display of
		        continuous-valued data in track format.  This
		        is useful for GC percent, probability scores,
		        and transcriptome data.
			Please see the
			
		        WIG description help page and the 
		        
		        custom tracks page for more details.
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