Hey,

I am analyzing RNA-seq data and I am interested in duplicated reads. I know I can count number of duplicated reads overall using picard markDuplicates.

samtools view -f 1024 dedup_reads.bam | wc -l

But i am interesting in the distribution of these duplicated. I have both sam and bam files.

Here is simple what i would to have

               # total reads              #duplicated reads          
   Gene1         30                                 10
   Gene2        100                                20
   Gene3         20                                 0

I googled but i couldn't find any tools, is there any tools, softwares or packages? Or should I implement myself.