I have used top hat in galaxy to map my files. After mapping i am interested in removing sequence duplicates from mapped .bam files. For this purpose i have used samtools - Rmdup. My problem is that when i checked sequence duplication levels in .bam file (processed by Rmdup) using FASTQC, it is again showing high sequence duplication level.
Same is the case with Picard:Markduplicates. It is also not removing duplicates (although remove_duplicates has been set to yes).
Please help me what i am doing wrong.