Complex Drosoohila Fosmid

Discuss issues with installing phred, phrap, and consed finishing packages.
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kstemler
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Joined: Fri Aug 17, 2007 5:21 pm
Location: University of Evansville
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Complex Drosoohila Fosmid

Post by kstemler » Thu Jan 24, 2008 5:15 pm

We are in the middle of training the students how to use Consed in finishing. Today, the students have been working on the Complex Drosophila Fosmid. Only one student has been able to join some of the contigs successfully, but has been unable to reproduce her results. Is there something wrong with the tutorial? No one else is able to follow the directions to combine the fosmids correctly. The major problem exists when we try to incorporate contig 46 into the main assembly. When the sequence trace is observed, it's of a very poor quality. Are there some other directions that we are missing in order to join these contigs, because 46 does not seem to span the gap. Thanks for whatever help we can recieve on this issue.

cshaffer
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Location: Washington University in St Louis
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Post by cshaffer » Sun Jan 27, 2008 4:19 am

I assume you are talking about clone 7G24?

This is a very tricky clone. We realized after the last workshop that the position of the tear is critical. If you don't tear in the right place you will not be able to follow along with the lecture notes and will get very different results. We have rewritten the help file that goes with this clone and expanded this part with explicit instructions on exactly where to make the tear if you want to follow along. This is posted on the GEP web site under sequence improvement, its the tutorial link under Complex dorosphila fosmid.

http://gep.wustl.edu/curriculum/course_ ... Fosmid.pdf

An important lesson that you can instruct your students here is that tearing in different places can give very different results. There is really no way to know in advance where to tear. As explained to me by the finishers, its all trial and error. So they would try a tear and then see if that leads to a solution, if not they try a different tear, and so on.

The good news is there should not be any of these types of clones in the pipeline for claiming, if any student does get a clone like this for their project be sure to seek help ASAP. We will be there to help guide you and the student through a difficult clone.

kstemler
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Post by kstemler » Sun Jan 27, 2008 8:11 pm

Thank you. After much toil we were able to join the contigs successfully. I'm sure that everyone has learned that the position of the tear is critical from this past exercise.

cshaffer
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Location: Washington University in St Louis
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my mistake

Post by cshaffer » Mon Jan 28, 2008 4:23 pm

Actually the tutorial link on the gep web page is the first update which was completed late last fall. There is an even newer version which is just being completed which should get posted in a week or two. It has even more updates with more of the curriculum that was only in the Mouse worksheet to make it possible to cover all the recommended curriculum with drosophila examples.

It should go up within 24 hours

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