fosmid ends vs. "primers too far apart"

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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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fosmid ends vs. "primers too far apart"

Post by cjones » Fri Apr 20, 2007 3:24 am

I've found that more than half of my students were confused by the triangle under their contigs which connects the ends of the fosmid. This normally indicates problems of assembly when consed determines that the two primers are too far apart -- and because it apparently thinks the fosmid has the same ca. 2-kb size limit as the subclones, it naturally marks this. Students spent a fair bit of time tearing and re-assembling trying to reconcile this "problem." Is there some way to perhaps change the read names for fosmid-terminal reads so that consed doesn't know that they come from the ends of the same piece of DNA?
Chris Jones
Assoc. Prof. of Biology
Moravian College
Bethlehem PA

cshaffer
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Joined: Sun Feb 04, 2007 10:29 pm
Location: Washington University in St Louis
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tag fosmid reads

Post by cshaffer » Mon Apr 23, 2007 3:55 pm

Good idea. This will take a non trivial amount of coding on our end to add more information to file names. It will also require that everyone who want this feature will need to update some of the locally installed perl scripts.

We just hired an undergrad to code for us all summer. I am hoping to have him work on these kinds of issues for the 10 weeks he is with us.

So, everyone please post more ideas if you have them, I don't know how productive he will be but I want to keep him busy coding all summer. So I want a avoid short "to do" list if I can.

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