I have mapped my RNA seq reads to the genome using tophat2. Thought eh mapping rate was 80%, it has been reported ~35 % has multiple alignments. By default, for multi-read(reads aligning to multiple locations), based on the alignment score, the best read is selected. For multi-read with same alignment score, tophat will report random alignment.
I would like to find how many multi-read has same alignment score from bam/sam file.
Also is there any possibility to assign the multi-read with same alignment score to best location.
Kindly guide me