Question: Markduplicate single end reads miRNA seq data
gravatar for aangajala
9 months ago by
aangajala0 wrote:

I am trying to analyze a RNA seq, single end SRA dataset. For this do i have to perform Markduplicates as it was mentioned in the tutorial bellow. When i do so, I am seeing 70-80% duplicates.In the example provided in the tutorial, it was less than 10% for paired end data.I am wondering if I should perform markduplicate, considering it is a single end data.Please advice. Do i have to do anything different considering micro RNA sequencing data as compared to tutorial.

Thank you.

rna-seq • 265 views
ADD COMMENTlink modified 9 months ago by Jennifer Hillman Jackson25k • written 9 months ago by aangajala0
gravatar for Jennifer Hillman Jackson
9 months ago by
United States
Jennifer Hillman Jackson25k wrote:


For very short reads, especially single-end reads, removing duplicates is not straightforward. I would suggest skipping this step in the analysis but you should also consider advice from sources with a specific focus on this type of analysis (publications, and possibly general bioinformatics forums like


Thanks, Jen, Galaxy team

ADD COMMENTlink written 9 months ago by Jennifer Hillman Jackson25k
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