Hi Juerg, Please see my comments below! Thanks! Best regards, Julie On 6/15/10 11:25 AM, "Straubhaar, Juerg" <juerg.straubhaar at="" umassmed.edu=""> wrote: > Hi Julie, > > I have a question on the output of annotatePeakInBatch (package chippeakanno): > > I have this output: > > space start end width names > peak strand feature > start_position end_position insideFeature distancetoFeature > shortestDistance > > 4 1 183100342 183100651 310 MACS_peak_1003 ENSMUSG00000062169 > MACS_peak_1003 1 ENSMUSG00000062169 183081062 18309912 > downstream 19280 1217 > > > fromOverlappingOrNearest > > NearestStart > > > My interpretation:: > > insideFeature: downstream: the TSS is downstream of the peak start, ok > The peak is downstream of the TSS > distancetoFeature: 19280, the TSS starts 19280nt downstream from start of peak > (start column), ok > The distance from the peak start to TSS > shortestDistance: 1217, distance to where? fromOverlappingOrNearest says > NearestStart, but nearest start is 19280nt ? > Minimum of (abs(peak start - feature start), abs(peak start - feature end), abs(peak end - feature start), abs(peak end - feature end)) where abs is short for absolute value. Please note that TSS is the feature start when the feature is on plus strand and the feature end when the feature is on minus strand. > Kind regards, > Juerg