Tophat Vs. Bowtie: Quality Scores

Question

[Justin]

I received 2 .bam files that were obtained from DNA-seq (they processed it with bowtie2) and RNA-seq (processed with TopHat). Let's call those DNA.bam and RNA.bam

Is it normal that in the RNA.bam file, the quality scores I see are only 0, 1, 2, 3 or 50, but looking at DNA.bam, I see anything from 0 to 42.

Does this have to do with bowtie and TopHat having different ways to calculate quality score? Or am I missing something really obvious here?

Thank you,

Answer 1

[Devon Ryan]

Yes, that's normal. Tophat only assigns 5 MAPQ values, where 50 indicates a unique alignment.