what tools approprite for remove duplicate reads from BAM file in Usegalaxy

The FastQC shows the fail and high sequence Duplication Levels in BAM file result in RNASeq data. what tool should be used for remove duplicate and better QC of BAM.

Hey agrieng3,
I post you two training material: CLIP-Seq data analysis from pre-processing to motif detection and ATAC-Seq data analysis. They use UMI-tools deduplicate, or ** MarkDuplicates to filter for PCR duplicates. I hope this will help you.


Hi Flow, thanks for response.
I used the MarkDuplicates tool but after that FASTQC fail due to high duplicate, the output of didn’t change for filter duplicates.

Dear agrieng3,
Have you followed directly the ATAC-Seq training? Meaning, have you set this option of MarkDuplicates, * “If true do not write duplicates to the output file instead of writing them with appropriate flags set” to Yes?