Hi, This is my first time using the package, so maybe this is a naive question What is the distance cutoff used to find "nearest feature (gene, exon, miRNA,etc)" or there isn't any and I can filter on it after the mapping? thanks -- Lucia Peixoto PhD Postdoctoral Research Fellow Laboratory of Dr. Ted Abel Department of Biology School of Arts and Sciences University of Pennsylvania "Think boldly, don't be afraid of making mistakes, don't miss small details, keep your eyes open, and be modest in everything except your aims." Albert Szent-Gyorgyi [[alternative HTML version deleted]]

Lucia, If you type help(annotatePeakInBatch), you will see that there is a parameter "output" with three options. By default, it is set to nearestStart which will generate nearest features without any distance constraint. If you set "output" to one of the other two options, then the distance cutoff can be set by specifying "maxgap", e.g., 5000 as 5kb. Please let me know if this answers your questions. Best regards, Julie On 3/7/14 2:18 PM, "Lucia Peixoto" <luciap at="" iscb.org=""> wrote: > Hi, > This is my first time using the package, so maybe this is a naive question > What is the distance cutoff used to find "nearest feature (gene, exon, > miRNA,etc)" > or there isn't any and I can filter on it after the mapping? > thanks