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Question: Markduplicate single end reads miRNA seq data
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gravatar for aangajala
9 months ago by
aangajala • 0
aangajala • 0 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. https://galaxyproject.org/tutorials/ngs/

Thank you.
rna-seq • 265 views
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modified 9 months ago by Jennifer Hillman Jackson ♦ 25k • written 9 months ago by aangajala • 0
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gravatar for Jennifer Hillman Jackson
9 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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 https://www.biostars.org).

Tutorial: https://galaxyproject.org/tutorials/ngs/#sampling-coincidence-duplicates

Thanks, Jen, Galaxy team
ADD COMMENT • link written 9 months ago by Jennifer Hillman Jackson ♦ 25k
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