After converting a 454 SFF file to FASTQ, I get sequences like this:
Key sequence, barcode, forward primer are all OK, but the last nucleotide of (the reverse complement of) the reverse primer is always lower case:
Because of this, it gets deleted when I do a trimmed conversion from SFF to FASTQ, and the sequence gets lost when my software looks for primers and barcodes. This has been happening for several 454 runs the last couple of months.
I can of course easily work around this, but still I would like to know what is causing this. Anybody has an idea?