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Old 06-29-2015, 03:08 PM   #2
Location: Prague, Czech Republic

Join Date: Nov 2010
Posts: 40

The 'agagcgaa' sequence is probably a custom MID (barcode). They (somebody at the sequencing centre) properly used the left trimpoint to delineate it. sff_extract does the right job as far as I can see.

I do not believe that anybody used 'AAAAAAAC' as a barcode as you say. That would be a good joke ... to design a homopolymer into a barcode for this platform (and also IonTorrent). Either way, the barcode would have to be visible in the sequence you showed but it is not. Nobody wrote a tool to edit the SFF files and slice them (only tools to 'mask' the existing sequence exist) so that is another reason why I do not believe somebody gave you SFF files with barcodes physically removed. Also, your sequence starts with the sequencing key 'tcag' so another reason to believe this is just the original, raw read sequence.

Last edited by martin2; 06-29-2015 at 03:12 PM.
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