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  • szy0931
    Member
    • Aug 2015
    • 51
    #1

    what should I do to the overrepresented reads

    I have some overrepresented reads in my RNA-Seq for Salmonella
    1. ssrA
    2. genomic DNA
    3. short reads (<20 bp), they are not adapter sequence and were not found in Salmonella genome by blast
    What should I to the sequence

    1. I do not care expression of ssrA. Should I leave them or remove them ?
    2. For overrepresented genomic DNA. Removing will result in losing real peaks. Should I just leave it?
    3. The short reads do not have hits on genomic. Should I just leave them or remove them?
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