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Unitas

unitas [-h] [-d CDS] [-u UNSPLICED_TRANSCRIPTOME]
                        [-r [REFSEQ [REFSEQ ...]]] [-s SPECIES]
                        path_to_rnas

positional arguments:
  path_to_rnas          Path to the folder with varying length RNAs in

optional arguments:
  -h, --help            show this help message and exit
  -d CDS, --cds CDS     Optional CDS region, passed to unitas
  -u UNSPLICED_TRANSCRIPTOME, --unspliced-transcriptome UNSPLICED_TRANSCRIPTOME
                        Optional, unspliced transcriptome, passed to unitas
  -r [REFSEQ [REFSEQ ...]], --refseq [REFSEQ [REFSEQ ...]]
                        References for use with unitas
  -s SPECIES, --species SPECIES
                        Species to set in unitas arguments

Input files:

  • path_to_rnas - path to the directory containing fastq files of each set of small RNAs you want to procesus in unitas

Note: to get unitas to work, you need to set either the species to a compatible species or provide one or more files of reference small RNAs. These can either be done with the -s and -r optional arguments or by adding them to your configuration file (see below).

  • CDS - Coding sequence, pipeline automatically labels with Gene and combines with the unspliced transcriptome, optional

  • unspliced_transcriptome - Unspliced transcriptome, pipeline automatically labels with Gene and combines with the CDS, optional

Output files:

  • unitas/ - directory containing the results for all the unitas runs performed by the program

  • unitas_summery.csv - CSV file containing the combined summaries of all of the unitas runs (plus some extra numbers). It is recommended to open it in a spreadsheet package (e.g. microsoft excel, libreoffice calc) as there is a lot of data and it may look a mess in a text editor.

  • UnitasGraph.png - graph showing the categories allocated by unitas against the length of the small RNA

  • unitas_graph_data.csv - raw data used for creating unitasGraph.png to allow for easy regraphing