Editing Nanopore RNA Sequencing Protocol (section)

=====Preparing Reference for EpiNano=====

One final thing that we want to do: we need to generate the appropriate files required to be able to run ''EpiNano'' later. This can be done by navigating to the folder containing your genome assembly (mine is at <code>~/Research/Ref</code>) and running a few lines of code (if you have files ending in <code>.fa.fai</code> and <code>.fa.dict</code> already in that folder for your assembly, you can skip this step). If you do not have a genome reference assembly yet, you may grab one from the [https://www.ncbi.nlm.nih.gov/projects/genome/guide/human/index.shtml NIH available here].

{{warning|The command <code>faidx</code> and <code>picard</code> may not run if you don’t have the appropriate software installed. You’ll know if it is installed or not when you try to execute it. If you do not have either of these installed, you can install <code>faidx</code> with the command <code>sudo apt install python3-pyfaidx</code> (''Linux''). <code>Picard</code> will need to be downloaded from the [https://github.com/broadinstitute/picard/releases/tag/2.27.4 Picard github here] as well (select the <code>picard.jar</code> file and place it into your root folder).}}

<code>Bash</code>
<syntaxhighlight lang="Bash">
sudo apt install python3-pyfaidx
</syntaxhighlight>

Next, we need to make the appropriate sequence libraries. This can be done as follows. Keep in mind that your paths may be different than the ones listed here!

<code>Bash</code>
<syntaxhighlight lang="Bash">
cd ~/Research/Ref
faidx GRCh38.p13.genome.fa
cd ~/Research/
java -jar picard.jar CreateSequenceDictionary \
      -R ~/MOP2/anno/GRCh38.p13.genome.fa \
      -O ~/MOP2/anno/GRCh38.p13.genome.fa.dict
</syntaxhighlight>

{{tip|The <code>picard.jar</code> file will need to be in the current working directory for the above code to work. If it isn’t found, make sure you place it in your ''Terminal'' working directory before attempting the code again, or switch your ''Terminal'' directory to the location of your <code>picard.jar</code> file with the <code>cd</code> command. Alternatively, you can make a shell shortcut to <code>picard.jar</code> by specifying the path.}}