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Discrepancy in paired-end Illumina data

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  • Discrepancy in paired-end Illumina data

    I have a variety of paired end data sets from Illumina and these are some of their sequence lengths:
    Read1 Read2
    103 110
    103 107
    101 101
    98 107
    Can anyone explain to me, why read1 and read2 have different sequence lengths for some datasets?
    Thanks,
    Vishal

  • #2
    It's pretty unusual to get this from a standard Illumina run (you can make up a custom recipe to do it though).

    Could the samples have had custom barcodes on the front of the first read, which have been stripped before returning the sequence to you?

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