Editing Nanopore RNA Sequencing Protocol (section)

===Check Read Count===

''Samtools'' comes with the ability to check the total number of reads in a <code>.bam</code> file via the command <code>view -c</code>. Therefore, at this stage you should count the total number of reads in both the master aligned file and (if aligned to the genome) the individual chromosome you isolated. This can be done via the following:

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

Or, if mapped to the transcriptome:

<code>Bash</code>
<syntaxhighlight lang="Bash">
samtools view -c ${SAMPLEID}_taligned.bam
</syntaxhighlight>

For reference, the <code>FAM95931</code> sample (identified here by ''flow cell'' ID) we ran had about 1.9 million reads total and 106,000 reads across chromosome 19. This was using a standard ''MinION'' flow cell, ''not'' a flongle, which should have about 120-200k reads.