When I run Tophat2 on human genome, I am using default parameters and with a GTF file from ensemble.
The accepted hits bam file has only three Mapping quality scores in 5th column in my file i.e 0, 3, 50. I would like to know is this correct or I have done something wrong.
As per my knowledge, mapping quality of 0 means the read mapped at multiple places but for other reads, I could see only 3 and 50. The data is from Illumina HiSeq 1000, paired end library.
I would be happy if anybody could help me in figuring out why I am getting only three figures .