Parameter Name | Default Value | Parameter Range | Description |
|---|---|---|---|
REF_FILE | file from which the reference annotation (GTF format) is read | ||
LOAD_CODING | true | {true,false} | flag to dis-/consider transcripts that have an annotated coding sequence |
LOAD_NONCODING | true | {true,false} | flag to dis-/consider transcripts that are annotated to be non-coding |
PRO_FILE | file to which the simulated expression values are written | ||
LIB_FILE | file to which the expressed transcript molecules are written |