This mode is used to create the read to weight map. This class scans a compact reads file to determine which heptamer occurs at the beginning of each read. When a heptamer is found that exists in the heptamer to weight data structure provided as input (see heptamer-weights mode to generate this data structure), the read is associated to the heptamer weight in a map. This map is written as Java serialized file for use with modes that estimate gene/transcript/exon/other counts. It is implemented by edu.cornell.med.icb.goby.modes.ReadsToWeightsMode.

Mode Parameters

The following options are available in this mode

FlagArgumentsRequiredDescription
(-o|--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. When several reads files are processed (of if argument is absent), the map filename is build dynamically from by removing the reads file extension and adding .id-weights, where id designates the type of weight estimation method used.
(-e|--heptamer-info)heptamer-infonoThe name of the file that contains heptamer information. Required when the heptamer weight method is used.
--methodmethodnoThe weight estimation method. Valid methods include heptamers, GC, AT, A, T,
C, G. Default value: heptamers
n/ainputyesThe basenames of the input alignments to concatenate.
--color-spacen/anoWhen this switch is provided, the reads are in color-space. Default value: FALSE