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  • Split seq data based on index AND barcode

    Dear all,

    I am currently designing an experiment, where my samples will have both a barcode and an index.
    Barcode: Sample-specific
    Index: Reaction-specific (here: ChIP reaction)

    So I might have X samples with each a unique barcode pooled together with the same index (A). And then Y samples with each a unique barcode pooled together with the same index (B).

    Can anyone advice me on the best way to perform demultiplexing on this type of data?

    I will specify the index on the sample sheet (here A or B), but then how to get the reads that are sample-specific, that is what I don't know how to do.

    I am hoping to get help to find an established tool for this.

    (sequencing will be done on MiSeq, HiSeq and/or NovaSeq)
    Last edited by Meyana; 01-26-2020, 08:25 PM.

  • #2
    Could you describe where your barcodes/indices are located in the Illumina reads?
    In the index reads (i5 and i7) or in-line with the forward and reverse sequence reads?

    Comment


    • #3
      Once you separate your sample pools based on Illumina demultiplexing you can then use a tool called sabre to demultiplex individual samples from the pool.

      Comment

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