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general:computerenvironment:software:rnaquast_step_by_step [2023/04/24 11:56] – freyageneral:computerenvironment:software:rnaquast_step_by_step [2025/05/02 06:58] (current) – [Running rnaQUAST] freya
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 ===== Installation of rnaQUAST ===== ===== Installation of rnaQUAST =====
  
-<WRAP important> Please install rnaQUAST with the following instructions +  * Create an anaconda environment for rnaQUAST and install it in the new environment.<WRAP> 
-<code> +<code>conda create --name "quastbusco"
-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 +
-</code> +
- +
-/*</WRAP> +
- +
-    * Create an anaconda environment for rnaQUAST with pyton 3.8 and install it in the new environment.<WRAP><code>  +
-conda create --name "quastbusco"+
 conda activate quastbusco conda activate quastbusco
  
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     * If you forgot the commands for this, remember that you can always google the conda cheat sheet.*/     * If you forgot the commands for this, remember that you can always google the conda cheat sheet.*/
  
-Next, test your installation by running:+  * Next, test your installation by running:<WRAP>
 <code> <code>
 #this will create an output-folder in your current directory: #this will create an output-folder in your current directory:
 rnaQUAST.py --test rnaQUAST.py --test
-</code>+</code></WRAP>
  
  
-===== Installation of BUSCO =====+===== 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. 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.
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         * Document your choice and your reasoning. Discuss with your colleagues if you're not sure.         * Document your choice and your reasoning. Discuss with your colleagues if you're not sure.
  
-    * Install BUSCO into your rnaQUAST environment using conda. +    * Identify the appropriate BUSCO data set from the list that you obtain with <WRAP><code>busco --list</code></WRAP> 
-    * Download and unzip the appropriate BUSCO data set from the [[https://busco-archive.ezlab.org/v3/|BUSCO webpage]]+    * Download the chosen data set with the following command: <WRAP><code>busco --download <NAME_OF_DATASET></code></WRAP>
  
 ===== Running rnaQUAST ===== ===== Running rnaQUAST =====
-    * Try to extract all the parameters you need from the [[http://cab.spbu.ru/files/rnaquast/release1.5.2/manual.html|rnaQUAST manual]] and run rnaQUAST +    * Try to extract all the parameters you need from the [[https://github.com/ablab/rnaquast|rnaQUAST github page]] and run rnaQUAST
-    * Remember that it is always a good idea to test your commands with small input files!+
  
 <WRAP> <WRAP>
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     * Run this command in your rnaQUAST conda environment:     * Run this command in your rnaQUAST conda environment:
 <code> <code>
-#This is just a suggestion, feel free to add any parameters that strike you as useful  +rnaQUAST.py --transcripts </path/to/>Trinity.fasta --busco </path/to/buscoset_odb12> -o </home/practixeXX/path/to/output>
-rnaQUAST.py --transcripts /home/practiceXX/path/to/Trinity.fasta --busco_lineage /home/practiceXX/path/to/buscoset_odb10 -o /home/practixeXX/path/to/output+
 </code> </code>
 </hidden> </hidden>
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 ===== Interpretation of the rnaQUAST output ===== ===== Interpretation of the rnaQUAST output =====
  
-    * Have a look at the test output and try to interpret it with the [[http://cab.spbu.ru/files/rnaquast/release1.5.2/manual.html|rnaQUAST manual]]. Document what you learned about the usage of rnaQUAST.+    * 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      * After the rnaQUAST + BUSCO run has finished, interpret and document the results. As always, try to 
         - State your expectations         - State your expectations
         - Summarize the results         - Summarize the results
         - Discuss           - Discuss