<p>I&#39;m using Tophat to align RNA-Seq reads to a genome. I want to know how many reads aligned, but I didn&#39;t know about the -g option when I ran Tophat, so the normal commands like &quot;samtools -c accepted_hits.bam&quot; isn&#39;t giving me the number of unique reads in the file, it&#39;s giving me the total number of alignments. Is there any way I can get this information without re-running Tophat?</p>

<p><code>samtools view -c -F 256 accepted_hits.bam</code></p>
