====== Running rnaQUAST + BUSCO step by step ======


===== Installation of rnaQUAST =====

  * Create an anaconda environment for rnaQUAST and install it in the new environment.<WRAP>
<code>conda create --name "quastbusco"
conda activate quastbusco

#install rnaQUAST
conda install -c bioconda rnaquast
</code> </WRAP>
    * If you forgot the commands for this, remember that you can always google the conda cheat sheet.*/

  * Next, test your installation by running:<WRAP>
<code>
#this will create an output-folder in your current directory:
rnaQUAST.py --test
</code></WRAP>


===== Running 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 [[https://busco.ezlab.org/|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:
            - Which BUSCO dataset contains more genes, the one of the eukaryotes or the one of the plants?
            - 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.

    * Identify the appropriate BUSCO data set from the list that you obtain with <WRAP><code>busco --list</code></WRAP>
    * Download the chosen data set with the following command: <WRAP><code>busco --download <NAME_OF_DATASET></code></WRAP>

===== Running rnaQUAST =====
    * Try to extract all the parameters you need from the [[https://github.com/ablab/rnaquast|rnaQUAST github page]] and run rnaQUAST

<WRAP>
<hidden Spoiler>
    * Run this command in your rnaQUAST conda environment:
<code>
rnaQUAST.py --transcripts </path/to/>Trinity.fasta --busco </path/to/buscoset_odb12> -o </home/practixeXX/path/to/output>
</code>
</hidden>
</WRAP>


===== Interpretation of the rnaQUAST output =====

    * Have a look at the test output and try to interpret it with the [[https://github.com/ablab/rnaquast|rnaQUAST github page]]. 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 
        - State your expectations
        - Summarize the results
        - Discuss