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fake reads

Posted: Wed Mar 10, 2010 2:21 pm
by chauser

We have a project that still has a gap DGA38L22 (we'll see if reads today close it).
We decided to try to make a fake read to either design primers from, or to close the gap itself.
-blasted 2 contigs vs grimshawii (flybase)
-identified grimshawii scaffold coordinates that span the gap
-pulled up the scaffold sequence (image below) (flybase)
-make fake reads

We actually managed to make fake reads which was pretty cool using the sequence identified and it matches reads in our assembly (good).

However, I believe n's in a scaffold assembly indicate a gap - is that right?
If so, are we working off of different assemblies?
Is this a valid approach?
The digests give us an estimate for gap size, and we are working based on these estimates.