Regarding new eCLIP processed data

The Yeo Lab and the ENCODE DCC have released new eCLIP processed files. These new bed, bigBed, and bigWig files include a supersedes property within its metadata to indicate which file it has replaced. Dr. Eric Van Nostrad (Yeo Lab) has provided the following statement in regards to the replacement:

“We improved the peak calling background detection to avoid issues of false negatives at a specific class of RNAs with short introns. There are very few old peaks that are not found in the new version (i.e., were few false positives in the old set); but there are some datasets with substantially increased number of peaks."

Please contact the ENCODE DCC help desk for any questions.