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  • ian.d.reid
    Junior Member
    • May 2009
    • 3
    #1

    5' cap and RNA-Seq

    How does the presence of a 5' cap on mRNA affect RNA-Seq processing? (I'm especially interested in Illumina sequencing.) Is the cap removed during mRNA preparation or fragmentation? If the cap persists, does it interfere with PCR, attachment to the flow cell, or sequencing? Does poor detection of capped fragments contribute to the tailing off of read coverage at 5' ends of transcripts?

    I haven't found any useful information about this through Pubmed or Google, but I bet someone here knows the answers.
    Tags: 5' cap, illumina, mrna, rna-seq
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