Split seq data based on index AND barcode

Meyana · 01-26-2020, 08:19 PM

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)

luc · 01-26-2020, 11:05 PM

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?

GenoMax · 01-27-2020, 05:10 AM

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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01-26-2020, 08:19 PM	#1
Meyana Member Location: Japan Join Date: Sep 2017 Posts: 40	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 08:25 PM.

01-26-2020, 11:05 PM	#2
luc Senior Member Location: US Join Date: Dec 2010 Posts: 452	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?

01-27-2020, 05:10 AM	#3
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	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.