Default parameters

The parameters and options decribed below are all optional. All parameters and options have default values that do not normally need to be modified.

Important

Ribotools parameters are changed via the configuration file, but options for programs such as Flexbar and STAR are handled via command line arguments. You do not need to include Ribotools parameters in the configuration file, unless you wish to change their values.

Flexbar and STAR options

For default parameters, consult the Rp-Bp documentation, in particular Flexbar and STAR options.

Caution

Providing --post-trim-length as a --flexbar-options will overwrite --trim-rna-to-max-fragment-size.

Note

Default STAR options are used for both Ribo-seq and trimmed RNA-seq reads. Unless you use --trim-rna-to-max-fragment-size, or to change the mapping parameters, use --star-options to override defaults, and run Ribo-seq and RNA-seq separately.

Ribotools parameters

For default parameters, consult the Rp-Bp documentation, in particular Rp-Bp parameters (general, shared MCMC, and metagene and periodicity estimation parameters).

HTSeq

Default options are overridden via command line using --htseq-options.

  • format Default: bam.

  • stranded Default: no.

  • type Default: CDS.

  • idattr Default: gene_id.

  • additional-attr Default: gene_name.

  • mode Default: intersection-nonempty.

  • secondary-alignments Default: ignore.

  • supplementary-alignments Default: ignore.