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About adapter trimming

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  • About adapter trimming

    Hi, everyone. I have a question regarding the adapter trimming of reads generated by Miseq. I am doing RNA seq using the Illumina RNA sample prep kit V2 and the sequencing reagents were V3-150 cycles. When preparing the sample sheet with IEM, I choose both “Use Adapter Trimming” and “Use Adapater Trimming Read 2” options. The resulting raw reads were about 75~76 bp. Is it necessary to further trim the reads before mapping to the reference genome or de novo assembly? I am using the CLC Genomics Workbench V8.0 for all analysis.

    Thank you.

  • #2
    You shouldn't have to. But if you are in "should double check this" category then you could pass them through a trim cycle one more time.