This mode is used to convert a full genome counts archive to the BedGraph format. The result can be imported into the UCSC genome browser to visualize counts in the context of genome annotations. It is implemented by edu.cornell.med.icb.goby.modes.CountsArchiveToBedGraphMode.java.

Mode Parameters

The following options are available in this mode

FlagArgumentsRequiredDescription
n/ainputyesThe counts archive basename to use as input.
(-o|--output)outputnoThe filename to output wiggle format counts.
(-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
(-l|--label)labelnoThe label to use as track name. Defaults to the basename of the counts file.
(-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).