NOTE! This is a read-only copy of the ENCODE2 wiki.
Please go to the ENCODE3 wiki for current information.
March 2009 Workshop
Summary of the AWG session from the meeting prepared by Jessica Melone (NHGRI).
Some action points from the AWG sesssion below. A word version of the straw man paper proposal from the session is available.
- ENCODE analysis will not move to GRC37 (hg19) until late this year at the earliest.
- Peak callers to be used for consistency are PeakSeq + SPP. (This was an arbitrary decision; coin toss)
- To enable comparison of data from different assays, a defined method for processing signal data will be used. (Signal data will be fed into segmentation/integration by taking tagAlign and having a single integer extension rule (which might be 0)).
- Paper plans:
- Focus on data from Tier 1 cells; use data from Tier 2 cells to test hypotheses.
- Tom Gingeras and John Stamatoyannopoulos will provide a list of hypotheses the data could be used to test (in preparation for the paper).
- Kate Rosenbloom will announce when final submission of Tier 1 datasets (a data freeze deadline) will take place. [This data freeze likely to take place in May 2009.]
- The AWG should look to use ENCODE data to explain GWAS data as part of the paper.
- Ross Hardison will lead on group to compile high quality functional annotations to compare to Tier 1 data.
- The ENCODE AWG should meet again in the summer of 2009 to present joint analysis results on the frozen Tier 1 datasets.
- Prior to the ENCODE AWG summer meeting, additional working groups (i.e., GWAS, peaks, etc.) should be formed to begin data analysis discussions.