Used the samstat tool (http://samstat.sourceforge.net/) for seeing the mapq scores of my alignment;
First, I used with the accepted_hits.bam, and found some reads classified as unmmaped. And, I thought strange. Shouldn't the accepted hits contain only mapped reads?
Second, When I use the samstat against unmapped reads.bam, all reads are 30 + mapq scored.
Can someone explain this to me?