Parameter

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

Overview

The "Gene Expression" step employs the annotation specified by REF_FILE_NAME and creates an artificial expression profile of the described transcripts. By the flag LOAD_CODING transcripts with an annotated coding sequence are taken into account, by LOAD_NONCODING correspondingly those which don't. Results from in silico gene expression are stored in the files specified by the parameters PRO_FILE respectively LIB_FILE; if no explicit values are provided for these parameters, then the corresponding files are created in the folder of the parameter file.

Details

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