Get # of unique mapped reads from Tophat output

Question

[colin.kern]

I'm using Tophat to align RNA-Seq reads to a genome. I want to know how many reads aligned, but I didn't know about the -g option when I ran Tophat, so the normal commands like "samtools -c accepted_hits.bam" isn't giving me the number of unique reads in the file, it's giving me the total number of alignments. Is there any way I can get this information without re-running Tophat?

Answer 1

[Devon Ryan]

samtools view -c -F 256 accepted_hits.bam