This mode is used to convert annotations to counts. Annotations can be used to represent segments of the reference sequences. This is can used to represent boundaries of exons on the chromosome sequences or the boundary of any other chromosomal region(s). This mode converts annotation files to the count format, setting count within the regions defined by the annotations to 1 and zero outside of the annotated regions. It is implemented by edu.cornell.med.icb.goby.modes.AnnotationsToCountsMode.java.

Mode Parameters

The following options are available in this mode

FlagArgumentsRequiredDescription
(-o|--output)outputnoThe name of the output basename to write the count archive. Default value: output-basename
(-f|--flanking-size)flanking-sizenoExtend captured regions by this number of bases on either side. Default value: 100
n/ainputyesThe basenames of the input alignments
(-v|--verbose)n/anoVerbose. For instance, reports when annotation segments are joined because they overlap. Default value: FALSE