Hi Abi, Set output ="both" will output the overlapping features within 1000 bp gap as well as the nearest feature calculated as peakstart to feature start despite the maxgap. If you only want the overlap feature within 1000bp gap, you should use output = "overlapping". Best regards, Julie On 5/6/10 10:32 AM, "Lakshmanan, Abirami" <abirami.lakshmanan@umassmed.edu> wrote: Hi Juile, When I use "annotatedPeakInBatch" ,output ="both", maxgap =1000 . My results would include all the overlaps and nearest start within 1000 bp on either side. Right? But I have highlighted the shortest distance to nearest starts which my output shows and they are very large( -300753) apart form the normal ones. Why does this happen? query: NCE_final_me1_co_T= annotatePeakInBatch(myexp, AnnotationData = NCE_final.rangedData, output="both", multiple=T, maxgap = 1000) Result: 1 1 35428 36965 1538 1331 NCE_122722 1331 1 NCE_122722 336181 336230 upstream -300753 299216 NearestStart 2 1 58428 60293 1866 1332 NCE_122722 1332 1 NCE_122722 336181 336230 upstream -277753 275888 NearestStart 3 1 60734 61364 631 1333 NCE_122722 1333 1 NCE_122722 336181 336230 upstream -275447 274817 NearestStart 4 1 67543 68063 521 1334 NCE_122722 1334 1 NCE_122722 336181 336230 upstream -268638 268118 NearestStart 5 1 76486 78310 1825 1335 NCE_122722 1335 1 NCE_122722 336181 336230 upstream -259695 257871 NearestStart Thanks, Abi [[alternative HTML version deleted]]