Does anyone know precisely how the barcodes embedded within ABI / Ambion's small RNA adapters are designed to work?
The 6nt barcoded regions appear to be buried deep within the adapters such that one needs to sequence a full 25nts of the 3' adapter (through what they call the "internal adapter" in the kit manual) in order to get to the barcodes. Given a 21nt small RNA, this would require a full 49 nts of reads to get to the barcode which does not seem feasible given the 35nt read-length of SOLiD runs. In the manual, it is stated that the barcodes are not yet supported by the SOLiD software but will be in the future. But it seems logical that one could manually separate different barcoded libraries by parsing differential adapter sequences at the end of the inserts for a given library.
for reference, I am referring to the SOLiD Small RNA expression kit marketed by ABI as cat # 4397682
The 6nt barcoded regions appear to be buried deep within the adapters such that one needs to sequence a full 25nts of the 3' adapter (through what they call the "internal adapter" in the kit manual) in order to get to the barcodes. Given a 21nt small RNA, this would require a full 49 nts of reads to get to the barcode which does not seem feasible given the 35nt read-length of SOLiD runs. In the manual, it is stated that the barcodes are not yet supported by the SOLiD software but will be in the future. But it seems logical that one could manually separate different barcoded libraries by parsing differential adapter sequences at the end of the inserts for a given library.
for reference, I am referring to the SOLiD Small RNA expression kit marketed by ABI as cat # 4397682
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