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  • Non-Barcoded reads. Why?

    Hello everybody!

    I am pretty new in the NGS jungle and I am struggling with the making sense of some NGS data. I hope someone can help me out:

    I have built a library with internal Barcodes which looks like the following:
    SolexaP5-NNNN-Barcode-NNNN-DNAinsert-SolexaP3
    N=random nucleotides to collapse PCR duplicates
    SolexaP5:AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
    SolexaP3:CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATC


    Unfortunately, after Barcode splitting, I noticed that I have many reads with no Barcode.

    Does any of you have an explanation why I get such non-barcoded reads?

    Any input would be much appreciated

    Thanks in advance!

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