I am currently analyzing a set of sequences obtained from a 454 pyrosequencing run. The sequences sent for sequencing were amplicons resulting from a substraction experiment aiming to target differentially methylated fragments.
The chimeric reads I am interested in have had some form of adapter-to-adapter ligation concatenate two sequences together, IE:
Adapter-(Seq-1-NNNNNNNN)-Adapter-(Seq-2-NNNNNNN)-Adapter
The tools I've found for identifying chimeric sequences all seem to require some kind of "reference sequences" be supplied, something I do not have. I am therefore looking for a tool which would look for mid-sequence adapters, and split the sequences it identifies accordingly.
Does anyone know of such a tool? If none exist, I will probably code some form of pipeline which BLASTs the adapter sequences and uses the results to split the sequences.
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not sure. But 454 paired-end does read in a single read both ends right? Was the 454 data paired-end? Then splitting for that should have been done automaticaly for you by the 454 data provider but you should be able to do it with Roche software most likely.
My 454 data is not paired-end, and I do not have access to Roche's software. Sequencing was performed off-facility, and all I received was an sff file along with an .fna and .qual file.