How to add a config fileΒΆ

Create separate YAML configuration files, or a single YAML configuration file, for Ribo- and RNA-seq. For Ribo-seq, consult How to add a config file.

Note

Required keys such as fasta and ribosomal_fasta are required only if you use Rp-Bp to create annotations, see How to prepare annotations.

For RNA-seq, additional keys are required:

  • rnaseq_samples (required, input) A dictionary key: value, where key is used to construct filenames, and value is the full path to the FASTQ.gz file for a given sample. The key should not contain spaces or special characters.

  • matching_samples (optional, input) A dictionary key: value, where key is the same as rnaseq_samples key, and value is the same as riboseq_samples key (matched samples). Required when using --trim-rna-to-max-fragment-size.

  • rna_adapter_file (optional, input) Path to adapter sequences to be removed (FASTA).

  • rnaseq_data (required, output) The base output location for all created files.

  • rnaseq_sample_name_map (optional, output) A dictionary key: value, where key is the same as rnaseq_samples key, and value is a fancy name for key to use in downstream analyses.

For TE or DE analyses, the following keys are required:

  • contrasts (required, input) A dictionary key: value, where key is a name for the contrast to be tested, and value contains 2 items, the first item is the condition to be tested against the second (reference).

  • tea_data (required, output) The base output location for all created files (TE).

  • dea_data (required, output) The base output location for all created files (DE).

  • sample_table (optional, input) The path to a sample table e.g. if running the analysis from existing data.

  • count_table (optional, input) The path to a count table e.g. if running the analysis from existing data.

Attention

Use sample_table and/or count_table only if these files are already available, e.g. to estimate TE or DE using existing sample and/or count tables. To automatically create these tables from the output of the pipeline, do not use these keys.

To download an example configuration file, check the test dataset included with the Tutorials, or consult the examples How to prepare the sample table for TE or How to prepare the sample table for DE. To change the default parameters, see Default parameters.