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 |
Parameter Name | Default Value | Parameter Range | Description |
---|---|---|---|
TSS_MEAN | 25 | >0 | rate of the exponential for deviation of simulated transcription starts from annotated transcription start point |
POLYA_SCALE | 300 | >0 | scale parameter of the Weibull distribution describing poly-A tail lengths |
POLYA_SHAPE | 2 | >0 | shape paramter of the Weibull distribution describing poly-A tail lengths |
Input: Columnn 6 of the PRO_FILE, i.e., the absolute number of RNA molecules that is simulated for a certain transcript in the experiment and the parameters of transcription start (TSS_MEAN) and poly-A tail variation (POLYA_SCALE, POLYA_SHAPE).
Output: One line per simulated transcript molecule containing in the LIB_FILE.