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local assembly, how to proceed?
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22 months ago
gbl1 • 70


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

rad-seq illumina • 129 views

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