Editing Nanopore RNA Sequencing Protocol (section)

===R File Paths===

<code>R</code>
<syntaxhighlight lang="R">
SAMPLEID="FAR91556"
GREFERENCEID="GRCh38.p14.rna.fna"
CHR="chr19"
OUTPUT_PATH=paste("/home/tj/Research/Data/Nanopore/Aligned", SAMPLEID, "", sep = "/")
M6ANET_PATH=paste("/home/tj/Research/Data/Nanopore/m6ANet_results", SAMPLEID, "", sep = "/")
</syntaxhighlight>

Note that at any time, you can check these in Terminal using the <code>echo</code> command. For example, if I wanted to check what my current <code>SAMPLEID</code> was, I would type <code>echo "${SAMPLEID}"</code> and execute. Also, notice that here we are only defining one sample to be analyzed, which is all we need for ''m6ANet'' or ''EpiNano-SVM''. ''EpiNano-Error'', however, requires two samples as input if you use it. For that analysis, I will leave defining the samples to be compared at the start of the ''EpiNano-Error'' section.