Running rnaQUAST + BUSCO step by step

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

• Create an anaconda environment for rnaQUAST with pyton 3.8 and install it in the new environment.

   
  conda create --name "quastbusco"
  conda activate quastbusco
  
  #install rnaQUAST
  conda install -c bioconda rnaquast

• If you forgot the commands for this, remember that you can always google the conda cheat sheet.

Next, test your installation by running:

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

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

• 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

• 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