phrap ignoring "do not overlap" command

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cjones
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Joined: Sun Feb 04, 2007 10:19 pm
Location: Moravian College, Bethlehem PA
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phrap ignoring "do not overlap" command

Post by cjones » Thu Feb 28, 2013 1:08 am

A student has labeled a problematic position with "tell phrap not to overlap discrepant reads at this position" (or whatever the literal command is) and then runs phredPhrap. Phrap has once again overlapped reads at this position -- how can we enforce this command? Tearing is of course an option, but it seems to me that it shouldn't be necessary (if we can get phrap to obey).
Chris Jones
Assoc. Prof. of Biology
Moravian College
Bethlehem PA

wleung
Posts: 185
Joined: Sun Feb 04, 2007 7:41 pm
Location: Washington University in St. Louis

Re: phrap ignoring "do not overlap" command

Post by wleung » Thu Feb 28, 2013 4:27 pm

The fact that phrap attempts to join the region you have tagged as "do not overlap" suggests the region have very high degree of similarity. This could mean that the discrepancy could be a polymorphism instead of a misassembly. To force phrap to not overlap a region, you can make more of the discrepancies artificially high quality (open the trace, middle click at the discrepant position and select 'Make High Quality') before you run phredPhrap. Alternatively, you can "Tell phrap to not overlap discrepant reads discrepant at this location" at discrepant positions surrounding the primary discrepancy.

For projects with complicated misassemblies, it might be easier to just manually tear the region apart and then use Miniassembly and Add New Reads instead of running phredPhrap to incorporate new data or reassemble a region.

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