This mode write annotations corresponding to a union of peaks accross each each input count archive. It is implemented by

edu.cornell.med.icb.goby.modes.CountsArchiveToUnionPeaksAnnotationMode.java.

Mode Parameters

The following options are available in this mode

FlagArgumentsRequiredDescription
n/ainputyesThe basenames of the count archives to read as input. If multiple count archives are provided, consensus peaks are called across the union of the input samples. The mode then outputs counts for these consensus peaks. This results in the same peak definitions being used across all the input samples.
(-o|--output)outputyesThe tab delimited output filename. The output will contain called peaks and peak count information.
(-r|--include-reference-names)include-reference-namesnoWhen provided, only write counts for reference identifiers listed in this comma separated list. To process only counts for chromosome 19 and 1, if sequences are identified by 1 and 19, use: --include-reference-names 1,19
(-a|--alternative-count-archive)alternative-count-archivenoSpecify an alternative count archive within the basename. The default is to use the count archive that ends in ".counts" (equivalent to -a counts). Default value: counts
(-t|--threshold)thresholdyesThe peak detection threshold. A peak boundary is called whenever the count at a specific base crosses the threshold. The defaulf value of one (1) indicates that a peak is called for any contguous segment of a reference sequence where the count is non-zero. Default value: 1
--peak-dist-thresholdpeak-dist-thresholdyesThe peak distance threshold for aggregation. Two neighboring peaks are aggregating if they are less than or equal to peak-dist-threshold away. Input should be in nucleotide base pairs (bp). Default value: 100