Parameters

Parameter

Name

Default

Value

Parameter

Range

Description
FRAGMENTATION
true{true,false}switches fragmentation on/off
FRAG_METHOD
UR{NB,UR,EZ}select the nebulization (NB), uniform-random fragmentation (UR), or enzymatic digestion (EZ) model
FRAG_SUBSTRATE
RNA{RNA,DNA}select whether fragmentation is carried out before (RNA) or after (DNA) reverse transcription
LIB_FILE_NAME
  the file from which fragments are read, and to which new fragments are written

Overview

Timepoint (FRAG_SUBSTRATE) and nature (FRAG_METHOD) of the fragmentation have to be chosen. Specific parameters then are required for each of the simulated fragmentation processes.

Details

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