Sarah, Please see my comments below. Best regards, Julie On 3/1/11 9:41 AM, "Sheppard, Sarah" <sarah.sheppard at="" umassmed.edu=""> wrote: > Hi Julie, > > I would like to use the annotatePeakInBatch function of ChIPpeakAnno to > identify the distance from a set of peaks to the end of 3'UTRs/transcripts. > > I was going to use these settings, but thought I'd check with you first to see > if you had any suggestions. > > Peaklist: my own peak data converted from bed format. is it correct that > strand information can only be as 1/-1? You can pass +/- for strand > AnnotationData: I'm using my own supplied data downloaded from BioMart, > transcript start and end > output: overlapping > multiple: true (in case there are multiple 3'UTR models or transcripts, will > one peak may map to both ensembl models?) Yes > maxgap: 100 (does this mean 100bp from the start/end coordinates of the > transcript?) Gap 100 means there is a gap of 100 bp (shortest distance) between your peak and the 3'UTR. > PeakLocForDistance: I want to use end, because this is where my polyA has been > cut off- Nathan thinks we should use the middle- can you make a suggestion > here? How long is your average peak? You could try both. > FeatureLocForDistance: end (because I want to know the distance of the peak > from the end of the transcript) > > Sure > Other options I was thinking about; because the distance to nearest feature > would then approximately be the length of the 3'UTR > > Annotation Data: coding sequence coordinates > output- overlapping > multiple: true > maxgap- would have to be larger e.g. 1500bp now for the peak to match up to > the end of the coding sequence, because these technically would not be > overlapping > PeakLocForDistance: same issue as above > FeatureLocForDistance: end > > > Annotation Data: 3'UTR coordinates. > output- both > multiple: true > maxgap- 100bp > PeakLocForDistance: same issue as above > FeatureLocForDistance: start > > Do you have any suggestions? > > Thanks, > > Sarah