Editing Nanopore RNA Sequencing Protocol (section)

====Getting Reference Transcriptome====

{{warning|A reference '''transcriptome''' is required for using ''m6ANet'', but you may choose to use the genome if you are using ''EpiNano''.}}

We will also need to download an appropriate reference transcriptome to map our reads to. I prefer to use the <code>GRCh38.p14</code> version, but you can use any you like. Just keep in mind that different reference assemblies may refer to transcripts or chromosomes using different IDs, which will change what you need to enter in the <code>${CHR}</code> (genome reference only) definition at the start of the protocol. Also, you can choose your own directory to place the reference transcriptome into, but just know that this path should also be updated in the <code>${REF}</code> shortcut in the Defining Files section above.

{{note|If the <code>wget</code> command is not available already on your system, you can install it with <code>sudo apt-get install wget</code>.}}

<code>Bash</code>
<syntaxhighlight lang="Bash">
cd "/home/$USER/Research/Ref"
wget "https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9606/110/GCF_000001405.40_GRCh38.p14/GCF_000001405.40_GRCh38.p14_rna.fna.gz"
gzip -d GCF_000001405.40_GRCh38.p14_rna.fna.gz
mv GCF_000001405.40_GRCh38.p14_rna.fna GRCh38.p14.rna.fna
</syntaxhighlight>

Note that here, I also renamed the transcriptome after extracting it for simplicity and ease of reference. A full list of all available genomes and transcriptomes can be accessed using the [https://ftp.ncbi.nlm.nih.gov/genomes/ NIH FTP], including older or more recent versions if you wish. You may also consider getting a reference genome / transcriptome from [https://useast.ensembl.org/index.html Ensembl] or [https://www.gencodegenes.org Gencode].