Page History
Parameter
Parameter Name | Default Value | Parameter Range | Description |
|---|---|---|---|
REF_FILE |
...
(1)
y=(x x 0 ) k exp −(x x 1 )−(x x 1 ) 2
where x denotes the rank number of a gene, x 0 the expression level of the highest abundant gene, and k and x 1 are cell type and/or experiment specific parameters. In the simulation, expression ranks are uniformly random assigned to transcripts of the reference, and subsequently their expression level in number of molecules and relative abundance is determined according to the law in Formula 1. Certainly, according to the corresponding settings a more or less substantial part of the transcripts from the reference annotation will remain unexpressed in the simulated run.
...
| 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
| Section |
|---|
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
| Section | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
|
Overview
Content Tools