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.
The following options are available in this mode
|n/a||input||yes||The counts archive basename to use as input.|
|(-o|--output)||output||no||The filename to output wiggle format counts.|
|(-r|--include-reference-names)||include-reference-names||no||When 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)||label||no||The label to use as track name. Defaults to the basename of the counts file.|
|(-a|--alternative-count-archive)||alternative-count-archive||no||Specify an alternative count archive within the basename. The default is to use the count archive that ends in ".counts" (equivalent to -a counts).|