RNA-Seq Command Line Options
|
Name |
Description |
Command Line Equivalent |
Range |
|---|---|---|---|
|
enable-rna |
Enable processing of RNA-seq data. |
--enable-rna |
true/false |
|
annotation-file |
Gene annotation file. Required for quantification and gene-fusion |
--annotation-file, -a |
Path to GTF (or .gtf.gz) file |
|
enable-rna-quantification |
Enable/disable RNA quantification. |
--enable-rna-quantification |
true/false |
|
rna-quantification-library-type |
Specifies the type of the RNA-seq library. Default is autodetect. |
--rna-quantification-library-type |
IU, ISR, ISF, U, SR, SF, orA. |
|
rna-quantification-gc-bias |
Correct for GC bias in fragment counts. |
--rna-quantification-gc-bias |
true/false |
|
enable-rna-gene-fusion |
Enable/disable RNA gene fusion calling. |
--enable-rna-gene-fusion |
true/false |
|
rna-gf-restrict-genes |
Ignore genes with biotype other than protein coding or lncRNA for gene fusions. |
--rna-gf-restrict-genes |
true/false |