Running rnaQUAST + BUSCO step by step

Please install rnaQUAST with the following instructions

conda create --name quastBusco python=3.8
conda activate quastBusco
conda install sepp=4.3.10
conda install -c conda-forge -c bioconda busco=5.3.2
conda install mamba
mamba install rnaquast
mamba install gmap=2020.10.14
rnaQUAST.py --test

Next, test your installation by running:

#this will create an output-folder in your current directory:
rnaQUAST.py --test

Installation of BUSCO

rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and gene database. In our case, we don't have a reference genome so we use a BUSCO set. The datasets of BUSCO contain only those genes which are shared between all members of a certain taxonomic group.

• Thinking of that, try to answer the following questions:
  1. Which BUSCO dataset contains more genes, the one of the eukaryotes or the one of the plants?
  2. Which BUSCO dataset should you choose for your rnaQUAST analysis? Try to have in mind what rnaQUAST is doing exactly and why we are using BUSCO in the first place.
• Document your choice and your reasoning. Discuss with your colleagues if you're not sure.

• Install BUSCO into your rnaQUAST environment using conda.
• Download and unzip the appropriate BUSCO data set from the BUSCO webpage

Running rnaQUAST

• Try to extract all the parameters you need from the rnaQUAST manual and run rnaQUAST
• Remember that it is always a good idea to test your commands with small input files!

#This is just a suggestion, feel free to add any parameters that strike you as useful 
rnaQUAST.py --transcripts /home/practiceXX/path/to/Trinity.fasta --busco_lineage /home/practiceXX/path/to/buscoset_odb10 -o /home/practixeXX/path/to/output

Interpretation of the rnaQUAST output

• Have a look at the test output and try to interpret it with the rnaQUAST manual. Document what you learned about the usage of rnaQUAST.
• After the rnaQUAST + BUSCO run has finished, interpret and document the results. As always, try to
  1. State your expectations
  2. Summarize the results
  3. Discuss