Editing Nanopore RNA Sequencing Protocol (section)

===Isolate Chromosome===

{{note|This step is ''ONLY'' for alignments that have been done to the genome and for processing with ''EpiNano''. If you are using ''m6ANet'', you’ll want to skip this portion.}}

This will speed up the ''EpiNano'' processing step substantially, since it will not be analyzing ''all'' of your data at once. ''Note that we defined the chromosome we wanted to isolate above at the start of the protocol'', with <code>${CHR}</code>.

<code>Bash</code>
<syntaxhighlight lang="Bash">
samtools view -b ${SAMPLEID}_aligned.bam ${CHR} > ${SAMPLEID}_${CHR}.bam
samtools index ${SAMPLEID}_${CHR}.bam ${SAMPLEID}_${CHR}.bam.bai
</syntaxhighlight>