rnaQUAST 0.1 manual

1. About rnaQUAST
2. Installation & Requirements
3. Options
    3.1. Input data options
    3.2. Basic options
    3.3. Advanced options
4. Feedback and bug reports

1 About rnaQUAST

rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and annotation. rnaQUAST version 0.1 was released under GPLv2 on March 7, 2015 and can be downloaded from http://bioinf.spbau.ru/en/rnaquast.

For impatient people:

 python rnaQUAST.py \
--transcripts /PATH/TO/transcripts1.fasta /PATH/TO/ANOTHER/transcripts2.fasta [...] \
--reference /PATH/TO/reference.fasta --annotation /PATH/TO/annotation.gtf

2 Installation & Requirements

To run rnaQUAST you need:

Note, that due to the limitations of blat, in order to work with reference genomes of size more than 4 Gb a pslSort is also required.

Path to pblat (and to pslSort if needed) executable should be included in $PATH environmental variable. To check that everything is installed correctly we recommend to run:

python rnaQUAST.py --test

3 Options

3.1 Input data options

To run rnaQuast one needs to provide either FASTA files with transcripts (recommended), or align transcripts to the reference genome manually and provide the resulting PSL files. rnaQUAST also requires reference genome and optionally an annotation.

-r <REFERENCE>, --reference <REFERENCE>
    Single file with reference genome containing all chromosomes/scaffolds in FASTA format.

-gtf <ANNOTATION>, --annotation <ANNOTATION>
    File with annotation in GTF/GFF format.

-c <TRANSCRIPTS ...>, --transcripts <TRANSCRIPTS, ...>
     File(s) with transcripts in FASTA format separated by space.

-psl <ALIGNMENTS ...>, --alignment <ALIGNMENTS, ...>
     File(s) with transcripts alignments in PSL format separated by space.

3.2 Basic options

-o <OUTPUT_DIR>, --output_dir <OUTPUT_DIR>
     Directory to store all results. Default is rnaQUAST_results/results_<datetime>.

--test
     Run rnaQUAST on the test data from the test_data folder, output directory is rnaOUAST_test_output.

-d, --debug
     Report detailed information, typically used only when detecting problems.

-h, --help
     Show help message and exit.

3.3 Advanced options

-t <INT>, --threads <INT>
     Maximum number of threads. Default is the number of CPU cores (detected automatically).

-l <LABELS ...>, --labels <LABELS ...>
     Names of assemblies that will be used in the reports separated by space.

-ss, --strand_specific
     Set if transcripts were assembled using strand specific RNA-Seq data in order to benefit from knowing whether the transcript originated from the + or - strand.

--min_alignment <MIN_ALIGNMENT>
     Minimal alignment size to be used, default value is 50.

--no_plots
     Do not draw plots (makes rnaQUAST run a bit faster).

4 Feedback and bug reports

Your comments, bug reports, and suggestions are very welcomed. They will help us to further improve rnaQUAST. If you have any troubles running rnaQUAST, please send us rnaquast.log from the output directory. Address for communications: rnaquast_support@ablab.spbau.ru.