Does accepted_hits.bam include unmapped.bam reads

[erichpeterson]

Does the accepted_hits.bam file generated by Tophat2 include those placed in unmapped.bam.

I ask because when I run:
samtools view accepted_hits.bam | cut -f1 | sort | uniq | wc -l

And then run:
cat sample.fq | wc -l
<result from previous command> / 4

The two values are exactly the same!

[marcowanger]

The short answer: nope

[erichpeterson]

The short answer: nope

I'm interested in the long answer. It is too much of a coincidence that these numbers are the same. I'm wanting to get a percentage of mapped reads and unmapped reads of the total number of reads.

Thanks