There are many blogs explaining the related post but none ended with a good solution, So I am posting with a new thread.
I want to know if there is any way to get information about number of reads uniquely mapped. Actually I found a code in a nature publication that gives number of uniquely mapped reads, but that was for single end reads. Now I am handling different projects in which some have paired end and some have single end data. In many of my data sets I get very less number of uniquely mapped reads (~10% of the total reads after removing duplicates). So to check it manually I tried counting number of unique combination of chromosome name & start positions & end positions, by converting my bam file into bed. But both the strategies are producing different numbers of uniquely mapped reads. So I want to know if there is any good and reliable way to count the uniques in any supported format. I aligned reads using bowtie2.