Phred phrap and re-assembling the reads

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jstamm
Posts: 30
Joined: Mon Aug 06, 2007 8:28 pm

Phred phrap and re-assembling the reads

Post by jstamm » Thu Feb 14, 2008 8:19 pm

Let's see if I can do this correctly...

Today was an interesting day. Here is another student's experience:

After adding new reads, phredphrap assembled the contigs opposite to how they originally were. The gap moved from the left side to the right side and then 2nd contig was complemented. Can you explain why this happened?

Assembly before:

Image


Assembly after:

Image

On a related note, is it possible to assemble two contigs when one of them is complemented and the other not, or should they always all either be tagged with the 'c' or not?

cshaffer
Posts: 211
Joined: Sun Feb 04, 2007 10:29 pm
Location: Washington University in St Louis
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phrap orientation

Post by cshaffer » Thu Feb 14, 2008 9:43 pm

The order and orientation of the contigs can flip with each new assembly by phrap. In fact I have seen different results with the same set of reads when assembled on two different computers.

In the above case I think you will find that contig 3 is flipped in the two assemblies. You can flip things around in any order you want using the reorder contigs or the reorient contigs under the "contig arrangement" button at the bottom of assembly view. These open dialog boxes where you can flip or reorder the contigs to get it they way you want.

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