This mode is used to evaluate heptamer weights following the method of Hansen et al, NAR April 2010. It is implemented by edu.cornell.med.icb.goby.modes.HeptamerWeightsMode.java.

Mode Parameters

The following options are available in this mode

FlagArgumentsRequiredDescription
(-c|--heptamer-counts)heptamer-countsnoThe filename where heptamer count statistics will be written (in tab delimited format). Default value: heptamer-counts.tsv
(-w|--weights)weightsnoThe filename where weights will be written for individual heptamers (in tab delimited format).
(-p|--map)mapnoThe filename where a map will be written that associates individual read indices (in the input) to weight. Such maps can for instance be used by alignment to transcript count to produce reweighted transcript counts. Default value: read-index-to-heptamer-weights.bin
(-o|--heptamer-info)heptamer-infonoThe filename where heptamer information will be written. This file contains enough information to map a set of new reads to weights. Default value: heptamer-info.bin
n/ainputyesThe basenames of the input alignments to concatenate.
--color-spacen/anoWhen this switch is provided, the reads are color-space and the first character of each read is skipped. Default value: FALSE