I prepared a library to run on illumina Hiseq but ended up sequencing it on a MinION sequencer (Oxford Nanopore Technologies). Since the output does not have barcodes in the header, I am having problems demultiplexing.
I did try using
grep to search for my adapters/barcodes but i get few reads. I also used
agrep with ambiguities and i get a lot more reads. but i cannot also retain the quality scores (the lines before the sequences.)
Any advice or direction to any already established pipelines for this would be greatly appreciated. Thanks!