Recommended Standards for Reporting mod/ENCODE Data
Version 1.0
January 23, 2009
Storing High Throughput Sequencing Data
• Image files from sequencing experiments do not need to be stored for the long term.
• Sequencing intensity files do not take up a lot of storage space and should be saved forthe long term.
Submitting mod/ENCODE Data
For ChIP-chip, DNase-chip/array, and FAIRE-chip:• Raw data should be submitted to GEO.
o Data should be flagged as being part of the mod/ENCODE project upon
submission to NCBI
• Processed data should be submitted to the relevant DCC as:o Ratio tracks
o Called peaks (see below)
o Metadata, including peak caller version used (see below)
For ChIP-seq, DNase-seq and FAIRE-seq:• Raw data should be submitted to GEO (1)o Data should be flagged as being part of the mod/ENCODE project through theuse of the appropriate genome project ID
o Each replicate should be submitted independently• Processed data should be submitted to the relevant DCC as:o Input signal or alignments (2) (will not be done for DNase/FAIRE Tier 3 lines)
o ChIP, DNase, and FAIRE signal or alignments (2)o Interpreted data signalo Called peaks (see below)
o FASTQ files (3)o Metadata, including peak caller version used (see below)• The DAC will propose how to generate gene target lists for ENCODE data. These lists
will be submitted to the DCC in the future.
Target Region and Peak Calling for ChIP, DNase and FAIRE Experiments
Point Source Peaks
For point source peaks (e.g., DNase, FAIRE, or signals from ChIP experiments withantibodies to sequence-specific transcription factors), common features that should bereported to the DCC are:• Peak, defined as a single base pair
• Start and end, defined as specific base pairs• Significance statistics using a three slot model (the inclusion of slots 2 and 3 is optional
for data submitters):• Slot 1: Signal value (e.g., fold enrichment) using an algorithm chosen by the submitter• Slot 2: P -value determined using a method chosen by the submittero Slot 3: Q-value (false discovery rate correction) determined using a method
chosen by the submitter• Metadata, including peak caller approach used (see below) and methods for determining
signal values, P-values, and Q-values, as applicableStandards for data reporting

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Broad Regions (does not pertain to DNase and FAIRE)• Start and end, defined as specific base pairs• Significance statistics using a three slot model (the inclusion of slots 2 and 3 is optional
for data submitters):• Slot 1: Average signal value across region (e.g.., fold enrichment) using an algorithm
chosen by the submitter• Slot 2: P -value determined using a method chosen by the submittero Slot 3: Q-value (false discovery rate correction) determined using a method
chosen by the submitter• Metadata, including peak caller approach used (see below) and methods for determining
signal values, P-values, and Q-values, as applicable• Point-source peaks can be called in addition to broad regions (i.e. one can have "peaks"
and potentially "valleys" within "regions").
It is up to the investigator to determine whether their data best fits the broad region/point
source peak data or both.
Metadata for Peak Caller
As an overall aim, mod/ENCODE should strive to provide public access to peak calling
software so outside data users can replicate the findings of the mod/ENCODE data
producers. Currently, peak calling software can be downloaded from the websites of theindividual data production groups and initially the consortium and should build on thisarrangement. In the longer term, it may be worthwhile to attempt to standardize peak andregion calling approaches so as to achieve optimal integration of data.
The metadata for each experiment should include a free form field where data producers arerequired to include information about the peak caller version that was used to produce the hitlist along with any information on parameters used for a particular experiment.
The modENCODE metadata field and ENCODE track documentation will be linked to a DCC
web page that lists the peak callers (and versions) that have been used for mod/ENCODE
data, which will in turn link to the websites maintained by the individual groups that allow for
the downloading of peak caller software by outside data users. Data producers are expected
to update information about peak calling software (including versions) on their websites assoon as new or updated software is implemented.
Notes:(1) NCBI intends for sequence data to be submitted directly to GEO. GEO will pass primary
sequence data to the SRA. If more convenient, data producers can make dual submissions
to the SRA and GEO. If this is done, sequences should be submitted to the SRA andmetadata, processed data, and a link to the SRA accession should be submitted to GEO.
(2) The ENCODE DCC will accept sequence alignments and/or signal graphs for input andChIP data. Sequence alignments will be posted for download, and will be loaded anddisplayed as a 'Counts graph' (count of tags overlapping each base) if no signal graph issubmitted.
(3) The ENCODE DCC will host FASTQ format sequence data and, where feasible, provide
co-located cluster computing for analysis since the GEO/SRA pipeline and access tools are
not mature enough at this stage to adequately support ENCODE analyses.

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