CATS-rb

Example usage

CATS-rb workflow consists of three scripts which should be run in succession:

Genome index generation script: CATS_rb_index

CATS-rb maps transcripts to the reference genome using Spaln. The first step is performed by CATS_rb_index, which generates the Spaln genome index for the reference genome. The reference genome does not need to be repeat-masked.

Example usage:

CATS_rb_index [OPTIONS] GENOME

Transcriptome assembly mapping script: CATS_rb_map

CATS_rb_map maps the analysed transcriptome assembly to the reference genome. The script should be run on all analysed assemblies individually.

Example usage:

CATS_rb_map [OPTIONS] GENOME_INDEX_DIR TRANSCRIPTOME

Mapping comparison script: CATS_rb_compare

CATS_rb_compare compares the mapped transcriptome assemblies. Optionally, a reference GTF/GFF3 gene annotation file can be supplied.

While CATS_rb_compare is primarily designed to compare multiple transcriptome assemblies, it can also be used with a single assembly. However, the output will not contain relative completeness analysis.

The most important optional parameters which should be set according to the analysed organism are maximum intron length (-i), maximum transcript set length for completeness analysis (-m), and the number of longest genomic scaffolds for exon set genomic location plot ( -f). See the detailed options section for further explanation.

Example usage without reference annotation:

CATS_rb_compare [OPTIONS] GENOME TRANSCRIPTOME_MAP_DIR ...

Example usage with reference annotation:

CATS_rb_compare -F GTF_FILE [OTHER_OPTIONS] GENOME TRANSCRIPTOME_MAP_DIR ...

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