The protocol recommends purifying 200 bp fragments from the gel. What if my fragments are not exactly 200 bps (when run on a Bioanalyzer)?
While 200 bp is the most ideal size for the GA system, this means the insert will be about 100 bp because the combined flanking sequence (including adaptors) will be about 100 bp. This will enable 35 bp to 50 bp single reads. NOTE: If the fragment is less than 150 bp, it may be difficult to obtain 50 bp reads.
