Dual barcodes in paired ened sequencing


I am preparing an oligos file to run trim.seqs from an Illumina run. Our approach uses dual indexing, in which both the fwd and rev primers are barcoded. This way, instead of using 200 fwd primers with unique barcodes (for 200 samples), we only use about 15 barcoded fwd and reverse primers and combine them so that each sample ends up unique combination. My problems is that if I prepare the oligos file using just the barcode in the fwd primer, there will be many samples with the same barcode. My questions are: 2. how can I enter the information for both barcodes in the oligos file? and 2. Will trim.seqs work in this scenario?




Can you email us at mothur.bugs@gmail.com? We have a feature that’s not quite ready for prime time that you will probably want to check out and we can walk you through how to use it.


Great! email sent.

Hi Pat,

Has this feature been released yet? I have a similar dataset to the one described here.