need some help in my 454 sequences data. I am using the function called "separate sequences by barcode" to sort through my multiplexed sequences. I have multiple individual barcodes in the pool. But I found the function did not keep the barcode in the sorted sequences (it automatically trimmed the barcode off after the sorting). I wonder if there are any function I can use to keep the barcode for later identification? I need those barcodes because I will have to pool two independent PCR sequences together later on, this way I can verify the sequences from PCR errors.
2) my second question is, if I have a second barcode at the end of the sequence, could I sort them through without convert them to reverse complementary sequences? (this procedure is what I am doing now)
Thanks a lot for the help!
Mark
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