Hi all. I received .fastq files from an overlapping-paires paired-end MiSeq run. I joined the pairs together using FLASH. However we used dual-indexing, so now I've got sequences that look like this
5' barcode1-link-primer1-----sequence-----primer2-link-barcode2 3'
(actually its more like
5' barcode1-link-primer1-----sequence-----2remirp-link-2edocrab 3' because of the reverse & join!)
So I need to demultiplex these (including primer removal). Does anybody know of any good programs that can demultiplex dual-indexed .fastq files? Any and all help much appreciated.
5' barcode1-link-primer1-----sequence-----primer2-link-barcode2 3'
(actually its more like
5' barcode1-link-primer1-----sequence-----2remirp-link-2edocrab 3' because of the reverse & join!)
So I need to demultiplex these (including primer removal). Does anybody know of any good programs that can demultiplex dual-indexed .fastq files? Any and all help much appreciated.
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