I've got reads from on kind of fragments to a linker on a restriction site. For each sample, I have 2 series with differant restriction enzymes.
Taken individually, I can assemble fragments up to 550bp. Most of them cannot be assembled.
A: ------------ B: ------------- C: -------------
Let's say A is the fragment after my specific primer, B and C are fragments on linker side for each enzyme. A and be are easilly assembled (for exemple with flash) but A and C cannot, because of the gap. If I assemble A and B, both end are fine, but C alone would have a left side sequence unsafe.
My aim is to take some (or all) A-B assemblies and to see if it can be extended by C fragments.
What is known: Orientation of fragments and which will be more precise. Cap3 won't work for it has to assemble on an unsafe side.
Any idea? Any suggestion?
Thanks to advance