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Old 01-26-2020, 07:19 PM   #1
Meyana
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Location: Japan

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Default 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 at 07:25 PM.
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Old 01-26-2020, 10:05 PM   #2
luc
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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?
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Old 01-27-2020, 04:10 AM   #3
GenoMax
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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.
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