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